Changeset 9087214 in sasview for src/sas/sasgui/perspectives


Ignore:
Timestamp:
Oct 11, 2016 11:09:47 AM (8 years ago)
Author:
jhbakker
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:
4581ac9, 7949dcf7
Parents:
392056d (diff), 46dfee9 (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 'master' into Jurrian1D, fingers crossed!

Location:
src/sas/sasgui/perspectives
Files:
9 added
1 deleted
14 edited
1 moved

Legend:

Unmodified
Added
Removed

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

    rd0248bd r0f7c930  
    181181        self.hint_sizer = wx.BoxSizer(wx.HORIZONTAL) 
    182182        self.qrange_sizer = wx.BoxSizer(wx.HORIZONTAL) 
    183         self.button_sizer = wx.BoxSizer(wx.HORIZONTAL) 
     183        self.button_sizer = wx.BoxSizer(wx.VERTICAL) 
     184        self.button_sizer1 = wx.BoxSizer(wx.HORIZONTAL) 
     185        self.button_sizer2 = wx.BoxSizer(wx.HORIZONTAL) 
    184186 
    185187    def _layout_data_name(self): 
    … …  
    392394        self.bt_close.SetToolTipString("Close this window") 
    393395 
    394         self.button_sizer.AddMany([(self.time_text , 0, wx.LEFT, 20), 
    395                                    (self.orient_combo , 0, wx.LEFT, 20), 
    396                                    (self.bt_compute, 0, wx.LEFT, 20), 
     396        self.button_sizer1.AddMany([(self.bt_compute, 0, wx.LEFT, 20), 
     397                                   (self.orient_combo , 0, wx.LEFT, 20)]) 
     398        self.button_sizer2.AddMany([(self.time_text , 0, wx.LEFT, 20), 
    397399                                   (self.bt_help, 0, wx.LEFT, 20), 
    398                                    (self.bt_close, 0, wx.LEFT, 5)]) 
     400                                   (self.bt_close, 0, wx.LEFT, 20)]) 
     401        self.button_sizer.AddMany([(self.button_sizer1 , 0, wx.BOTTOM|wx.LEFT, 10), 
     402                                   (self.button_sizer2 , 0, wx.LEFT, 10)]) 
    399403 
    400404    def estimate_ctime(self): 
    … …  
    600604                raise 
    601605            self.orient_combo.Show(is_pdbdata) 
    602             self.button_sizer.Layout() 
     606            #self.button_sizer.Layout() 
     607            self.FitInside() 
    603608            self._set_sld_data_helper(True) 
    604609        except: 

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

    rd85c194 rafb93df  
    33.. This is a port of the original SasView html help file to ReSTructured text 
    44.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015. 
     5.. Text revised during Code Camp V in Oct 2016. 
    56 
    6 Python Shell Tool 
    7 ================= 
     7.. _Python_shell: 
     8 
     9Python Shell-Editor Tool 
     10======================== 
    811 
    912Description  
    1013----------- 
    1114 
    12 This is a Python shell/editor (PyCrust) provided with WxPython. An editing  
    13 notebook will show up when a Python file is created/loaded with the *New* or  
    14 *Open* options on the menu.  
     15This is a Python shell/editor provided with WxPython. 
    1516 
    16 *Run* enables the editor to compile and run the Python code. 
     17For the help about Python, visit the website http://docs.python.org/tutorial/ 
    1718 
    18 For the details about the Python, visit the website http://docs.python.org/tutorial/ 
     19.. note:: This shell/editor has its own help, but the Help() and Credits() calls do not work on Macs. 
    1920 
    20 The NumPy, SciPy, and Matplotlib, etc, libraries are shipped with SasView.  
    21 However, some functionality may not work. 
     21The NumPy, SciPy, and Matplotlib, etc, libraries are shipped with SasView and so functions from these can be imported into the shell/editor, however, some functionality may not work. 
    2222 
    23 PyCrust has its own Help. 
     23.. image:: new_pycrust_example.png 
     24   :align: center 
    2425 
    25 *NOTE! The Help() and Credits() calls do not work on Macs.* 
     26When a Python file, for example a fitting model, is created or loaded with the *New* or *Open* options from the menu, a new tab opens with an editing notebook. 
    2627 
    27 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     28.. image:: new_pycrust_example_2.png 
     29   :align: center 
    2830 
    29 Example 
    30 ------- 
     31If a Python (.py) model has a linked C (.c) subroutine *in the same folder* then the shell/editor will open both! However input focus is usually transferred to the tab with the .c file. 
    3132 
    32 An example calling the Matplotlib plotting gallery: 
    33  
    34 .. image:: pycrust_example.png 
     33To compile a model, select *Run* > *Check Model* from the shell/editor menu. If the model contains a unit test (which it should!!!) then this will also run and a popup window will report the success/failure of the test. 
    3534 
    3635.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    3736 
    38 .. note::  This help document was last changed by Steve King, 19Feb2015 
     37.. note::  This help document was last changed by Steve King, 10Oct2015 

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

    r9501661 rec72ceb  
    7070 
    7171    This Dialog pops up for the user when they press 'Sum|Multi(p1,p2)' under 
    72     'Edit Custom Model' under 'Fitting' menu.  This is currently called as 
     72    'Plugin Model Operations' under 'Fitting' menu.  This is currently called as 
    7373    a Modal Dialog. 
    7474 

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

    r0912b405 rd472e86  
    103103    window_name = "Custom Model Editor" 
    104104    ## Name to appear on the window title bar 
    105     window_caption = "Custom Model Editor" 
     105    window_caption = "Plugin Model Editor" 
    106106    ## Flag to tell the AUI manager to put this panel in the center pane 
    107107    CENTER_PANE = False 
    … …  
    110110                    size=(PANEL_WIDTH, PANEL_HEIGHT)): 
    111111        self.config = None 
     112 
    112113        editor.EditorNotebookFrame.__init__(self, parent=parent, 
    113                                         title=title, size=size, 
    114                                         filename=filename) 
     114                                        title=title, size=size) 
    115115        self.parent = parent 
    116116        self._manager = manager 
    … …  
    126126        self.dataDir = dataDir 
    127127        self.Centre() 
     128 
     129        # See if there is a corresponding C file 
     130        if filename != None: 
     131            c_filename = os.path.splitext(filename)[0] + ".c" 
     132            if os.path.isfile(c_filename): 
     133                self.bufferCreate(c_filename) 
     134 
     135            # If not, just open the requested .py, if any. 
     136            # Needs to be after the C file so the tab focus is correct. 
     137            if os.path.isfile(filename): 
     138                    self.bufferCreate(filename) 
    128139 
    129140        self.Bind(wx.EVT_MENU, self.OnNewFile, id=wx.ID_NEW) 

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

    rda456fb r1404cce  
    1010 
    1111This performs a correlation function analysis of one-dimensional 
    12 SANS data, or generates a model-independent volume fraction profile from a 
    13 one-dimensional SANS pattern of an adsorbed layer. 
    14  
    15 The correlation function analysis is performed in 3 stages: 
     12SAXS/SANS data, or generates a model-independent volume fraction  
     13profile from the SANS from an adsorbed polymer/surfactant layer. 
     14 
     15A correlation function may be interpreted in terms of an imaginary rod moving  
     16through the structure of the material. Γ\ :sub:`1D`\ (R) is the probability that  
     17a rod of length R moving through the material has equal electron/neutron scattering  
     18length density at either end. Hence a frequently occurring spacing within a structure  
     19manifests itself as a peak. 
     20 
     21A volume fraction profile :math:`\Phi`\ (z) describes how the density of polymer segments/surfactant molecules varies with distance from an (assumed locally flat) interface. 
     22 
     23Both functions are returned in *real space*. 
     24 
     25The analysis is performed in 3 stages: 
    1626 
    1727*  Extrapolation of the scattering curve to :math:`Q = 0` and 
    1828   :math:`Q = \infty` 
    19 *  Fourier/Hilbert Transform of the extrapolated data to give the correlation 
    20    function/volume fraction profile 
    21 *  Interpretation of the 1D correlation function based on an ideal lamellar 
    22    morphology 
     29*  Smoothed merging of the two extrapolations into the original data 
     30*  Fourier / Hilbert Transform of the smoothed data to give the correlation 
     31   function / volume fraction profile, respectively 
     32*  (Optional) Interpretation of the 1D correlation function based on an ideal  
     33   lamellar morphology 
    2334 
    2435.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    2839 
    2940To :math:`Q = 0` 
    30 ^^^^^^^^^^^^^^^^ 
     41................ 
    3142 
    3243The data are extrapolated to Q = 0 by fitting a Guinier model to the data 
    33 points in the lower Q range. 
     44points in the low-Q range. 
     45 
    3446The equation used is: 
    3547 
    3648.. math:: 
    37     I(Q) = e^{A+Bq^2} 
     49    I(Q) = Ae^{Bq^2} 
    3850 
    3951The Guinier model assumes that the small angle scattering arises from particles 
    … …  
    4153particles. This has dubious applicability to polymer systems. However, the 
    4254correlation function is affected by the Guinier back-extrapolation to the 
    43 greatest extent at large values of R and so the back-extrapolation only has a 
    44 small effect on the analysis. 
     55greatest extent at large values of R and so only has a 
     56small effect on the final analysis. 
    4557 
    4658To :math:`Q = \infty` 
    47 ^^^^^^^^^^^^^^^^^^^^^ 
     59..................... 
    4860 
    4961The data are extrapolated to Q = :math:`\infty` by fitting a Porod model to 
    50 the data points in the upper Q range. 
     62the data points in the high-Q range. 
    5163 
    5264The equation used is: 
    5365 
    5466.. math:: 
    55     I(Q) = Bg + KQ^{-4}e^{-Q^2\sigma^2} 
    56  
    57 Where :math:`Bg` is the Bonart thermal background, :math:`K` is the Porod 
    58 constant, and :math:`\sigma > 0` describes the electron (or neutron scattering 
    59 length) density profile at the interface between crystalline and amorphous 
    60 regions (see figure 1). 
     67    I(Q) = K Q^{-4}e^{-Q^2\sigma^2} + Bg 
     68 
     69Where :math:`Bg` is the background, :math:`K` is the Porod 
     70constant, and :math:`\sigma` (which must be > 0) describes the width of the electron or neutron scattering length density profile at the interface between the crystalline and amorphous 
     71regions as shown below. 
    6172 
    6273.. figure:: fig1.gif 
    6374   :align: center 
    6475 
    65    **Figure 1** The value of :math:`\sigma` is a measure of the electron 
    66    density profile at the interface between crystalline and amorphous regions. 
    67  
     76    
    6877Smoothing 
    69 ^^^^^^^^^ 
    70  
    71 The extrapolated data set consists of the Guinier back-extrapolation up to the 
    72 highest Q value of the lower Q range, the original scattering data up to the 
    73 highest value in the upper Q range, and the Porod tail-fit beyond this. The 
    74 joins between the original data and the Guinier/Porod fits are smoothed using 
    75 the algorithm below, to avoid the formation of ripples in the transformed data. 
     78--------- 
     79 
     80The extrapolated data set consists of the Guinier back-extrapolation from Q~0  
     81up to the lowest Q value in the original data, then the original scattering data, and the Porod tail-fit beyond this. The joins between the original data and the Guinier/Porod fits are smoothed using the algorithm below to avoid the formation of ripples in the transformed data. 
    7682 
    7783Functions :math:`f(x_i)` and :math:`g(x_i)` where :math:`x_i \in \left\{ 
    … …  
    8793    h_i = \frac{1}{1 + \frac{(x_i-b)^2}{(x_i-a)^2}} 
    8894 
     95         
    8996Transform 
    9097--------- 
    9198 
    9299Fourier 
    93 ^^^^^^^ 
    94  
    95 If Fourier is selected for the transform type, the analysis will perform a 
     100....... 
     101 
     102If "Fourier" is selected for the transform type, the analysis will perform a 
    96103discrete cosine transform on the extrapolated data in order to calculate the 
    97 correlation function. The following algorithm is applied: 
     104correlation function 
     105 
     106.. math:: 
     107    \Gamma _{1D}(R) = \frac{1}{Q^{*}} \int_{0}^{\infty }I(q) q^{2} cos(qR) dq 
     108 
     109where Q\ :sup:`*` is the Scattering Invariant. 
     110 
     111The following algorithm is applied: 
    98112 
    99113.. math:: 
    … …  
    103117 
    104118Hilbert 
    105 ^^^^^^^ 
    106 If Hilbert is selected for the transform type, the analysis will perform a 
     119....... 
     120 
     121If "Hilbert" is selected for the transform type, the analysis will perform a 
    107122Hilbert transform on the extrapolated data in order to calculate the Volume 
    108123Fraction Profile. 
    109124 
     125.. note:: This functionality is not yet implemented in SasView. 
     126 
     127 
    110128Interpretation 
    111129-------------- 
    112 Once the correlation function has been calculated by transforming the 
    113 extrapolated data, it may be interpreted by clicking the "Compute Parameters" 
    114 button. The correlation function is interpreted in terms of an ideal lamellar 
    115 morphology, and structural parameters are obtained as shown in Figure 2 below. 
    116 It should be noted that a small beam size is assumed; no de-smearing is 
     130 
     131Correlation Function 
     132.................... 
     133 
     134Once the correlation function has been calculated it may be interpreted by clicking the "Compute Parameters" button. 
     135 
     136The correlation function is interpreted in terms of an ideal lamellar 
     137morphology, and structural parameters are obtained from it as shown below. 
     138It should be noted that a small beam size is assumed; ie, no de-smearing is 
    117139performed. 
    118140 
    119141.. figure:: fig2.gif 
    120142   :align: center 
    121  
    122    **Figure 2** Interpretation of the correlation function. 
    123143 
    124144The structural parameters obtained are: 
    … …  
    131151*   Local Crystallinity :math:`= L_c/L_p` 
    132152 
     153Volume Fraction Profile 
     154....................... 
     155 
     156SasView does not provide any automatic interpretation of volume fraction profiles in the same way that it does for correlation functions. However, a number of structural parameters are obtainable by other means: 
     157 
     158*   Surface Coverage :math:`=\theta` 
     159*   Anchor Separation :math:`= D` 
     160*   Bound Fraction :math:`= <p>` 
     161*   Second Moment :math:`= \sigma` 
     162*   Maximum Extent :math:`= \delta_{\text{h}}` 
     163*   Adsorbed Amount :math:`= \Gamma` 
     164 
     165.. figure:: profile1.png 
     166   :align: center 
     167  
     168.. figure:: profile2.png 
     169   :align: center 
     170    
     171 
     172References 
     173---------- 
     174 
     175Strobl, G. R.; Schneider, M. *J. Polym. Sci.* (1980), 18, 1343-1359 
     176 
     177Koberstein, J.; Stein R. *J. Polym. Sci. Phys. Ed.* (1983), 21, 2181-2200 
     178 
     179Baltá Calleja, F. J.; Vonk, C. G. *X-ray Scattering of Synthetic Poylmers*, Elsevier. Amsterdam (1989), 247-251 
     180 
     181Baltá Calleja, F. J.; Vonk, C. G. *X-ray Scattering of Synthetic Poylmers*, Elsevier. Amsterdam (1989), 257-261 
     182 
     183Baltá Calleja, F. J.; Vonk, C. G. *X-ray Scattering of Synthetic Poylmers*, Elsevier. Amsterdam (1989), 260-270 
     184 
     185:ref:`FDR` (PDF format) 
     186 
    133187.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     188 
    134189 
    135190Usage 
    136191----- 
    137192Upon sending data for correlation function analysis, it will be plotted (minus 
    138 the background value), along with a red bar indicating the lower Q range (used 
    139 for back-extrapolation), and 2 purple bars indicating the upper Q range (used 
    140 for forward-extrapolation) [figure 3]. These bars may be moved my clicking and 
    141 dragging, or by entering the appropriate values in the Q range input boxes. 
     193the background value), along with a *red* bar indicating the *upper end of the  
     194low-Q range* (used for back-extrapolation), and 2 *purple* bars indicating the range to be used for forward-extrapolation. These bars may be moved my clicking and 
     195dragging, or by entering appropriate values in the Q range input boxes. 
    142196 
    143197.. figure:: tutorial1.png 
    144198   :align: center 
    145199 
    146    **Figure 3** A plot of some data showing the Q range bars 
    147  
    148 Once the Q ranges have been set, click the "Calculate" button next to the 
    149 background input field to calculate the Bonart thermal background level. 
    150 Alternatively, enter your own value into the field. Click the "Extrapolate" 
    151 button to extrapolate the data and plot the extrapolation in the same figure. 
    152 The values of the parameters used for the Guinier and Porod models will also be 
    153 shown in the "Extrapolation Parameters" section [figure 4] 
     200Once the Q ranges have been set, click the "Calculate" button to determine the background level. Alternatively, enter your own value into the field. If the box turns yellow this indicates that background subtraction has resulted in some negative intensities. 
     201 
     202Click the "Extrapolate" button to extrapolate the data and plot the extrapolation in the same figure. The values of the parameters used for the Guinier and Porod models will also be shown in the "Extrapolation Parameters" section of the window. 
    154203 
    155204.. figure:: tutorial2.png 
    156205   :align: center 
    157206 
    158    **Figure 4** A plot showing the extrapolated data and the original data 
    159  
    160 Then, select which type of transform you would like to perform, using the radio 
     207Now select which type of transform you would like to perform, using the radio 
    161208buttons: 
    162209 
    163210*   **Fourier** Perform a Fourier Transform to calculate the correlation 
    164     function of the extrapolated data 
     211    function 
    165212*   **Hilbert** Perform a Hilbert Transform to calculate the volume fraction 
    166     profile of the extrapolated data 
    167  
    168 Clicking the transform button will then perform the selected transform and plot 
    169 it in a new figure. If a Fourier Transform was performed, the "Compute 
    170 Parameters" button can also be clicked to calculate values for the output 
    171 parameters [figure 5] 
     213    profile 
     214 
     215Click the "Transform" button to perform the selected transform and plot 
     216the result in a new graph window. 
     217 
     218If a Fourier Transform was performed, the "Compute Parameters" button can now be clicked to interpret the correlation function as described earlier. 
    172219 
    173220 .. figure:: tutorial3.png 
    174221    :align: center 
    175222 
    176     **Figure 5** The Fourier Transform (correlation function) of the 
    177     extrapolated data, and the parameters extracted from it. 
     223         
     224.. note:: 
     225    This help document was last changed by Steve King, 08Oct2016 

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

    r51a4d78 r9087214  
    10371037            dispersity = self.disp_box.GetClientData(n) 
    10381038            name = dispersity.__name__ 
    1039  
    10401039            self._set_dipers_Param(event=None) 
    10411040 
    … …  
    11081107        self.Refresh() 
    11091108 
     1109    def get_cat_combo_box_pos(self, state): 
     1110        """ 
     1111        Iterate through the categories to find the structurefactor 
     1112        :return: combo_box_position 
     1113        """ 
     1114        for key, value in self.master_category_dict.iteritems(): 
     1115            for list_item in value: 
     1116                if state.formfactorcombobox in list_item: 
     1117                    return self.categorybox.Items.index(key) 
     1118 
    11101119    def reset_page_helper(self, state): 
    11111120        """ 
    … …  
    11631172            category_pos = int(state.categorycombobox) 
    11641173        except: 
     1174            state.formfactorcombobox = unicode(state.formfactorcombobox.lower()) 
     1175            state.categorycombobox = unicode(state.categorycombobox) 
    11651176            category_pos = 0 
    1166             for ind_cat in range(self.categorybox.GetCount()): 
    1167                 if self.categorybox.GetString(ind_cat) == \ 
    1168                                         state.categorycombobox: 
    1169                     category_pos = int(ind_cat) 
    1170                     break 
     1177            if state.categorycombobox in self.categorybox.Items: 
     1178                category_pos = self.categorybox.Items.index( 
     1179                    state.categorycombobox) 
     1180            else: 
     1181                # Look in master list for model name (model.lower) 
     1182                category_pos = self.get_cat_combo_box_pos(state) 
    11711183 
    11721184        self.categorybox.Select(category_pos) 
    … …  
    11891201            structfactor_pos = int(state.structurecombobox) 
    11901202        except: 
    1191             structfactor_pos = 0 
    1192             for ind_struct in range(self.structurebox.GetCount()): 
    1193                 if self.structurebox.GetString(ind_struct) == \ 
    1194                                                     (state.structurecombobox): 
    1195                     structfactor_pos = int(ind_struct) 
    1196                     break 
     1203            if state.structurecombobox is not None: 
     1204                structfactor_pos = 0 
     1205                state.structurecombobox = unicode(state.structurecombobox) 
     1206                for ind_struct in range(self.structurebox.GetCount()): 
     1207                    if self.structurebox.GetString(ind_struct) == \ 
     1208                                                        (state.structurecombobox): 
     1209                        structfactor_pos = int(ind_struct) 
     1210                        break 
    11971211 
    11981212        self.structurebox.SetSelection(structfactor_pos) 
    … …  
    14071421        self.state.npts = self.npts_x 
    14081422 
    1409     def _onparamEnter_helper(self): 
     1423    def _onparamEnter_helper(self,is_modified = False): 
    14101424        """ 
    14111425        check if values entered by the user are changed and valid to replot 
    … …  
    14131427        """ 
    14141428        # Flag to register when a parameter has changed. 
    1415         is_modified = False 
     1429        #is_modified = False 
    14161430        self.fitrange = True 
    14171431        is_2Ddata = False 
    … …  
    14211435            is_2Ddata = True 
    14221436        if self.model != None: 
    1423             is_modified = (self._check_value_enter(self.fittable_param) 
    1424                            or self._check_value_enter(self.fixed_param) 
    1425                            or self._check_value_enter(self.parameters)) 
     1437            #Either we get a is_modified = True passed in because 
     1438            #_update_paramv_on_fit() has been called already or 
     1439            # we need to check here ourselves. 
     1440            if not is_modified: 
     1441                is_modified = (self._check_value_enter(self.fittable_param) 
     1442                               or self._check_value_enter(self.fixed_param) 
     1443                               or self._check_value_enter(self.parameters)) 
    14261444 
    14271445            # Here we should check whether the boundaries have been modified. 
    … …  
    14721490        flag = True 
    14731491        self.fitrange = True 
     1492        is_modified = False 
    14741493 
    14751494        #wx.PostEvent(self._manager.parent, StatusEvent(status=" \ 
    … …  
    14841503                                                                [self.data]) 
    14851504            ##Check the values 
    1486             self._check_value_enter(self.fittable_param) 
    1487             self._check_value_enter(self.fixed_param) 
    1488             self._check_value_enter(self.parameters) 
     1505            is_modified = (self._check_value_enter(self.fittable_param) 
     1506                            or self._check_value_enter(self.fixed_param) 
     1507                            or self._check_value_enter(self.parameters)) 
    14891508 
    14901509            # If qmin and qmax have been modified, update qmin and qmax and 
    … …  
    15681587            logging.error(traceback.format_exc()) 
    15691588 
    1570         return flag 
     1589        return flag,is_modified 
    15711590 
    15721591    def _reset_parameters_state(self, listtorestore, statelist): 
    … …  
    19791998            form_factor = self.formfactorbox.GetClientData(f_id) 
    19801999 
    1981         if form_factor is None or not form_factor.is_form_factor: 
     2000        if form_factor is None or \ 
     2001            not hasattr(form_factor, 'is_form_factor') or \ 
     2002            not form_factor.is_form_factor: 
    19822003            self.structurebox.Hide() 
    19832004            self.text2.Hide() 
    … …  
    23062327            wx.PostEvent(self.parent, event) 
    23072328        #draw the model with the current dispersity 
    2308         self._draw_model() 
     2329 
     2330        #Wojtek P, Oct 8, 2016: Calling draw_model seems to be unessecary. 
     2331        #By comenting it we save an extra Iq calculation 
     2332        #self._draw_model() 
     2333 
    23092334        ## Need to use FitInside again here to replace the next four lines. 
    23102335        ## Otherwised polydispersity off does not resize the scrollwindow. 
    … …  
    30553080        """ 
    30563081        content = '' 
     3082        bound_hi = '' 
     3083        bound_lo = '' 
    30573084        # go through the str params 
    30583085        for item in param: 
    … …  
    30863113                    value = item[2].GetValue() 
    30873114 
     3115            # Bounds 
     3116            try: 
     3117                bound_lo = item[5].GetValue() 
     3118                bound_hi = item[6].GetValue() 
     3119            except Exception: 
     3120                # harmless - need to just pass 
     3121                pass 
     3122 
    30883123            # add to the content 
    30893124            if disfunc != '': 
    … …  
    31013136            except Exception: 
    31023137                logging.error(traceback.format_exc()) 
    3103             content += name + ',' + str(check) + ',' + value + disfunc + ':' 
     3138            content += name + ',' + str(check) + ',' +\ 
     3139                    value + disfunc + ',' + bound_lo + ',' +\ 
     3140                    bound_hi + ':' 
    31043141 
    31053142        return content 
    … …  
    31523189                # Transfer the text to content[dictionary] 
    31533190                context[name] = [check, value] 
     3191 
     3192                # limits 
     3193                limit_lo = item[3] 
     3194                context[name].append(limit_lo) 
     3195                limit_hi = item[4] 
     3196                context[name].append(limit_hi) 
     3197 
    31543198            # ToDo: PlugIn this poly disp function for pasting 
    31553199            try: 
    3156                 poly_func = item[3] 
     3200                poly_func = item[5] 
    31573201                context[name].append(poly_func) 
    31583202                try: 
    31593203                    # take the vals and weights for  array 
    3160                     array_values = item[4].split(' ') 
    3161                     array_weights = item[5].split(' ') 
     3204                    array_values = item[6].split(' ') 
     3205                    array_weights = item[7].split(' ') 
    31623206                    val = [float(a_val) for a_val in array_values[1:]] 
    31633207                    weit = [float(a_weit) for a_weit in array_weights[1:]] 
    … …  
    32073251                name = item[1] 
    32083252                if name in content.keys(): 
    3209                     check = content[name][0] 
    3210                     pd = content[name][1] 
     3253                    values = content[name] 
     3254                    check = values[0] 
     3255                    pd = values[1] 
     3256 
    32113257                    if name.count('.') > 0: 
    32123258                        # If this is parameter.width, then pd may be a floating 
    … …  
    32313277                            fun_val = self.model.fun_list[content[name][1]] 
    32323278                            self.model.setParam(name, fun_val) 
     3279                    try: 
     3280                        item[5].SetValue(str(values[-3])) 
     3281                        item[6].SetValue(str(values[-2])) 
     3282                    except Exception: 
     3283                        # passing as harmless non-update 
     3284                        pass 
    32333285 
    32343286                    value = content[name][1:] 
    … …  
    32753327                                self.model.setParam(name, fun_val) 
    32763328                                # save state 
     3329                        try: 
     3330                            item[5].SetValue(str(value[-3])) 
     3331                            item[6].SetValue(str(value[-2])) 
     3332                        except Exception: 
     3333                            # passing as harmless non-update 
     3334                            pass 
     3335 
    32773336                        self._paste_poly_help(item, value) 
    32783337                        if check == 'True': 
    … …  
    33093368        """ 
    33103369        # Do nothing if not setting polydispersity 
    3311         if len(value[1]) == 0: 
     3370        if len(value[3]) == 0: 
    33123371            return 
    33133372 

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

    r7988501 r9087214  
    424424        self.Bind(wx.EVT_RADIOBUTTON, self.onSlitSmear, 
    425425                  id=self.slit_smearer.GetId()) 
    426         self.disable_smearer.SetValue(True) 
     426        self.enable_smearer.SetValue(True) 
    427427 
    428428        sizer_smearer.Add(self.disable_smearer, 0, wx.LEFT, 10) 
    … …  
    10581058            self.create_default_data() 
    10591059        """ 
    1060         flag = self._update_paramv_on_fit() 
    1061  
    1062         wx.CallAfter(self._onparamEnter_helper) 
     1060        flag,is_modified = self._update_paramv_on_fit() 
     1061 
     1062        wx.CallAfter(self._onparamEnter_helper,is_modified) 
    10631063        if not flag: 
    10641064            msg = "The parameters are invalid" 

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

    rff3f5821 rec72ceb  
    221221        self.id_edit = wx.NewId() 
    222222        editmodel_help = "Edit customized model sample file" 
    223         self.menu1.AppendMenu(self.id_edit, "Edit Custom Model", 
     223        self.menu1.AppendMenu(self.id_edit, "Plugin Model Operations", 
    224224                              self.edit_model_menu, editmodel_help) 
    225225        #create  menubar items 
    … …  
    236236        frame = PyConsole(parent=self.parent, manager=self, 
    237237                          panel=self.fit_panel, 
    238                           title='Advanced Custom Model Editor', 
     238                          title='Advanced Plugin Model Editor', 
    239239                          filename=filename) 
    240240        self.put_icon(frame) 
    … …  
    302302            event_id = event.GetId() 
    303303            dir_path = models.find_plugins_dir() 
    304             title = "New Custom Model Function" 
     304            title = "New Plugin Model Function" 
    305305            self.new_model_frame = EditorWindow(parent=self, base=self, 
    306306                                                path=dir_path, title=title) 
    … …  
    319319        Update custom model list in the fitpage combo box 
    320320        """ 
    321         custom_model = 'Customized Models' 
     321        custom_model = 'Plugin Models' 
    322322        try: 
    323323            # Update edit menus 
    … …  
    350350        wx_id = wx.NewId() 
    351351        #new_model_menu = wx.Menu() 
    352         self.edit_model_menu.Append(wx_id, 'New', 
     352        self.edit_model_menu.Append(wx_id, 'New Plugin Model', 
    353353                                   'Add a new model function') 
    354354        wx.EVT_MENU(owner, wx_id, self.make_new_model) 
    … …  
    362362        self.edit_menu = wx.Menu() 
    363363        self.edit_model_menu.AppendMenu(e_id, 
    364                                     'Advanced', self.edit_menu) 
     364                                    'Advanced Plugin Editor', self.edit_menu) 
    365365        self.set_edit_menu_helper(owner, self.edit_custom_model) 
    366366 
    … …  
    368368        self.delete_menu = wx.Menu() 
    369369        self.edit_model_menu.AppendMenu(d_id, 
    370                                         'Delete', self.delete_menu) 
     370                                        'Delete Plugin Models', self.delete_menu) 
    371371        self.set_edit_menu_helper(owner, self.delete_custom_model) 
    372372 
    373373        wx_id = wx.NewId() 
    374         self.edit_model_menu.Append(wx_id, 'Load Models', 
     374        self.edit_model_menu.Append(wx_id, 'Load Plugin Models', 
    375375          '(Re)Load all models present in user plugin_models folder') 
    376376        wx.EVT_MENU(owner, wx_id, self.load_plugin_models) 
    377  
     377                 
    378378    def set_edit_menu_helper(self, owner=None, menu=None): 
    379379        """ 

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

    r05829fb r46dfee9  
    33Fitting Documentation 
    44===================== 
     5 
     6.. note:: In Windows use [Alt]-[Cursor left] to return to the previous page 
    57 
    68.. toctree:: 
    … …  
    1820 
    1921   Information on the SasView Optimisers <optimizer.rst> 
    20  
    21    Writing a Plugin <plugin.rst> 
     22       
     23   Converting SANS to SESANS for Fitting <../../../sans_to_sesans> 
     24    
     25   Fitting SESANS Data <../../../sesans_fitting.rst> 
     26    
     27   Writing a Plugin Model <plugin.rst> 
     28       
     29   Computations with a GPU <../../../gpu_computations> 
     30    

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

    r05829fb r3e1c9e5  
    1818======= 
    1919 
     20.. note:: If some code blocks are not readable, expand the documentation window 
     21 
    2022.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    2123 
    … …  
    116118--------------- 
    117119 
    118 For a complete list of all the library models available in SasView, see the Model Documentation. 
     120For a complete list of all the library models available in SasView, see the `Model Documentation <../../../index.html>`_ . 
    119121 
    120122It is also possible to add your own models. 
    … …  
    124126.. _Adding_your_own_models: 
    125127 
    126 Adding your own models 
     128Adding your own Models 
    127129---------------------- 
    128130 
    129 There are currently two ways to add your own models to SasView: 
    130  
    131 * Using the :ref:`Custom_Model_Editor` 
    132 * By :ref:`Writing_a_Plugin` 
    133  
    134 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    135  
    136 .. _Custom_Model_Editor: 
    137  
    138 Custom Model Editor 
    139 ------------------- 
    140  
    141 From the *Fitting* option in the menu bar, select *Edit Custom Model*. 
    142  
    143 .. image:: edit_model_menu.bmp 
    144  
    145 and then one of the options 
    146  
    147 *  *New* - to create a new custom model template 
    148 *  *Sum|Multi(p1,p2)* - to create a new model by summing/multiplying existing models in the model library 
    149 *  *Advanced* - to edit a new custom model 
    150 *  *Delete* - to delete a custom model 
    151  
    152 New 
    153 ^^^^ 
     131There are essentially three ways to generate new fitting models for SasView: 
     132 
     133* Using the SasView :ref:`New_Plugin_Model` helper dialog (best for beginners and/or relatively simple models) 
     134* By copying/editing an existing model (this can include models generated by the *New Plugin Model* dialog) in the :ref:`Python_shell` or :ref:`Advanced_Plugin_Editor` (suitable for all use cases) 
     135* By writing a model from scratch outside of SasView (only recommended for code monkeys!) 
     136 
     137Please read the guidance on :ref:`Writing_a_Plugin` before proceeding. 
     138 
     139**To be found by SasView your model must reside in the *~\\.sasview\\plugin_models* folder.** 
     140 
     141.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     142 
     143.. _Plugin_Model_Operations: 
     144 
     145Plugin Model Operations 
     146----------------------- 
     147 
     148From the *Fitting* option in the menu bar, select *Plugin Model Operations* 
     149 
     150.. image:: edit_model_menu.png 
     151 
     152and then one of the sub-options 
     153 
     154*  *New Plugin Model* - to create a plugin model template with a helper dialog 
     155*  *Sum|Multi(p1,p2)* - to create a plugin model by summing/multiplying *existing models* in the model library 
     156*  *Advanced Plugin Editor* - to create/edit a plugin model in a Python shell 
     157*  *Delete Plugin Models* - to delete a plugin model 
     158*  *Load Plugin Models* - to (re-)load plugin models 
     159 
     160.. _New_Plugin_Model: 
     161 
     162New Plugin Model 
     163^^^^^^^^^^^^^^^^ 
    154164 
    155165.. image:: new_model.bmp 
    156166 
    157167A model template generated by this option can be viewed and further modified using 
    158 the :ref:`Advanced` option. 
     168the :ref:`Advanced_Plugin_Editor` . 
    159169 
    160170*NB: "Fit Parameters" has been split into two sections, those which can be 
    … …  
    167177.. image:: sum_model.bmp 
    168178 
    169 This option creates a custom model of the form 
    170  
    171 Custom Model = scale_factor \* (model1 +/\* model2) 
    172  
    173 In the *Easy Sum/Multi Editor* give the new custom model a function name and brief 
    174 description (to appear under the *Details* button on the *Fit Page*). Then select 
     179This option creates a custom model of the form:: 
     180 
     181     Custom Model = scale_factor \* {(scale_1 \* model_1) \+ (scale_2 \* model_2)} \+ background 
     182 
     183or:: 
     184 
     185     Custom Model = scale_factor \* model_1 \* model_2 \+ background 
     186 
     187In the *Easy Sum/Multi Editor* give the new model a function name and brief 
     188description (to appear under the *Details* button on the *FitPage*). Then select 
    175189two existing models, as p1 and p2, and the required operator, '+' or '*' between 
    176190them. Finally, click the *Apply* button to generate the model and then click *Close*. 
    177191 
    178 *NB: Any changes to a custom model generated in this way only become effective after* 
    179 *it is re-selected from the model drop-down menu on the Fit Page.* 
    180  
    181 .. _Advanced: 
    182  
    183 Advanced 
    184 ^^^^^^^^ 
    185  
    186 Selecting this option shows all the custom models in the plugin model folder 
    187  
    188   *C:\\Users\\[username]\\.sasview\\plugin_models* - (on Windows) 
     192Any changes to a plugin model generated in this way only become effective *after* it is re-selected from the model drop-down menu on the FitPage. 
     193 
     194.. _Advanced_Plugin_Editor: 
     195 
     196Advanced Plugin Editor 
     197^^^^^^^^^^^^^^^^^^^^^^ 
     198 
     199Selecting this option shows all the plugin models in the plugin model folder, on Windows this is 
     200 
     201  *C:\\Users\\{username}\\.sasview\\plugin_models* 
    189202 
    190203You can edit, modify, and save the Python code in any of these models using the 
    191 *Advanced Custom Model Editor*. 
    192  
    193 See :ref:`Writing_a_Plugin` for details on the plugin format. 
    194  
    195 *NB: Sum/Product models are still using the SasView 3.x model format.  Unless 
    196 you are confident about what you are doing, it is recommended that you 
    197 only modify lines denoted with the ## <----- comments!* 
    198  
    199 When editing is complete, select *Run -> Compile* from the *Model Editor* menu bar. An 
    200 *Info* box will appear with the results of the compilation and model unit tests. The 
    201 model will only be usable if the tests 'pass'. 
    202  
    203 To use the model, go to the relevant *Fit Page*, select the *Customized Models* 
     204*Advanced Plugin Model Editor*. Note that this is actually the same tool as the :ref:`Python_shell` . 
     205 
     206For details of the SasView plugin model format see :ref:`Writing_a_Plugin` . 
     207 
     208.. note:: Model files generated with the Sum/Multi option are still using the SasView 3.x model format. Unless you are confident about what you are doing, it is recommended that you only modify lines denoted with the ## <----- comments! 
     209 
     210When editing is complete, select *Run* > *Check Model* from the *Advanced Plugin Model Editor* menu bar. An *Info* box will appear with the results of the compilation and model unit tests. The model will only be usable if the tests 'pass'. 
     211 
     212.. image:: ../calculator/new_pycrust_example_2.png 
     213 
     214To use the model, go to the relevant *Fit Page*, select the *Plugin Models* 
    204215category and then select the model from the drop-down menu. 
    205216 
    206 *NB: Any changes to a custom model generated in this way only become effective after* 
    207 *it is re-selected from the model drop-down menu on the Fit Page.* 
    208  
    209 Delete 
    210 ^^^^^^ 
    211  
    212 Simply highlight the custom model to be removed. This operation is final! 
    213  
    214 *NB: Custom models shipped with SasView cannot be removed in this way.* 
     217Any changes to a plugin model generated in this way only become effective *after* it is re-selected from the model drop-down menu on the FitPage. 
     218 
     219Delete Plugin Models 
     220^^^^^^^^^^^^^^^^^^^^ 
     221 
     222Simply highlight the plugin model to be removed. The operation is final!!! 
     223 
     224*NB: Plugin models shipped with SasView cannot be removed in this way.* 
     225 
     226Load Plugin Models 
     227^^^^^^^^^^^^^^^^^^ 
     228 
     229This option loads (or re-loads) all models present in the *~\\.sasview\\plugin_models* folder. 
    215230 
    216231.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    600615.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    601616 
    602 .. note::  This help document was last changed by Steve King, 04Jun2015 
     617.. note::  This help document was last changed by Steve King, 10Oct2016 

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

    rb2a3814 r3e1c9e5  
    66.. note:: If some code blocks are not readable, expand the documentation window 
    77 
     8Introduction 
     9^^^^^^^^^^^^ 
     10 
     11There are essentially three ways to generate new fitting models for SasView: 
     12 
     13* Using the SasView :ref:`New_Plugin_Model` helper dialog (best for beginners and/or relatively simple models) 
     14* By copying/editing an existing model (this can include models generated by the *New Plugin Model* dialog) in the :ref:`Python_shell` or :ref:`Advanced_Plugin_Editor` as described below (suitable for all use cases) 
     15* By writing a model from scratch outside of SasView (only recommended for code monkeys!) 
     16 
    817Overview 
    918^^^^^^^^ 
    1019 
    11 You can write your own model and save it to the the SasView 
    12 *plugin_models* folder 
    13  
    14   *C:\\Users\\[username]\\.sasview\\plugin_models* (on Windows) 
    15  
    16 The next time SasView is started it will compile the plugin and add 
    17 it to the list of *Customized Models* in a FitPage.  It is recommended that an 
    18 existing model be used as a template. 
    19  
    20 SasView has three ways of writing models: 
    21  
    22 - As a pure python model : Example - 
     20If you write your own model and save it to the the SasView *plugin_models* folder 
     21 
     22  *C:\\Users\\{username}\\.sasview\\plugin_models* (on Windows) 
     23 
     24the next time SasView is started it will compile the plugin and add 
     25it to the list of *Plugin Models* in a FitPage. 
     26 
     27SasView models can be of three types: 
     28 
     29- A pure python model : Example - 
    2330  `broadpeak.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/broad_peak.py>`_ 
    24 - As a python model with embedded C : Example - 
     31- A python model with embedded C : Example - 
    2532  `sphere.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/sphere.py>`_ 
    26 - As a python wrapper with separate C code : Example - 
     33- A python wrapper with separate C code : Example - 
    2734  `cylinder.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/cylinder.py>`_, 
    2835  `cylinder.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/cylinder.c>`_ 
    … …  
    4249 
    4350In the *~\\.sasview\\plugin_models* directory, copy the appropriate files 
    44 (using the examples above as templates) to mymodel.py (and mymodel.c, etc) 
     51(we recommend using the examples above as templates) to mymodel.py (and mymodel.c, etc) 
    4552as required, where "mymodel" is the name for the model you are creating. 
    4653 
    … …  
    662669^^^^^^^^^^^^^^^^^^^ 
    663670 
    664 Installed SasView 
    665 ................. 
    666  
    667 If you are editing your model from the SasView GUI, you can test it 
    668 by selecting *Run > Check Model* from the *Model Editor* menu bar. An 
    669 *Info* box will appear with the results of the compilation and a 
    670 check that the model runs. 
    671  
    672  
    673 Built SasView 
    674 ............. 
     671Minimal Testing 
     672............... 
     673 
     674Either open the :ref:`Python_shell` (*Tools* > *Python Shell/Editor*) or the :ref:`Advanced_Plugin_Editor` (*Fitting* > *Plugin Model Operations* > *Advanced  
     675Plugin Editor*), load your model, and then select *Run > Check Model* from the  
     676menu bar. 
     677 
     678An *Info* box will appear with the results of the compilation and a check that  
     679the model runs. 
     680 
     681Recommended Testing 
     682................... 
    675683 
    676684If the model compiles and runs, you can next run the unit tests that 
    … …  
    793801consider adding your model to the 
    794802`Model Marketplace <http://marketplace.sasview.org/>`_ so that others may use it! 
     803 
     804.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     805 
     806.. note::  This help document was last changed by Steve King, 10Oct2016 

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

    r212bfc2 r5de7f69  
    181181            try: 
    182182                model = load_custom_model(path) 
     183                model.name = "[plug-in] "+model.name 
    183184                plugins[model.name] = model 
    184185            except Exception: 

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

    re6de6b8 r467202f  
    17531753 
    17541754        return doc 
     1755 
     1756# Simple html report templet 
     1757HEADER = "<html>\n" 
     1758HEADER += "<head>\n" 
     1759HEADER += "<meta http-equiv=Content-Type content='text/html; " 
     1760HEADER += "charset=windows-1252'> \n" 
     1761HEADER += "<meta name=Generator >\n" 
     1762HEADER += "</head>\n" 
     1763HEADER += "<body lang=EN-US>\n" 
     1764HEADER += "<div class=WordSection1>\n" 
     1765HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >" 
     1766HEADER += "%s</font></center></span></center></b></p>" 
     1767HEADER += "<p class=MsoNormal>&nbsp;</p>" 
     1768PARA = "<p class=MsoNormal><font size='4' > %s \n" 
     1769PARA += "</font></p>" 
     1770CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n" 
     1771CENTRE += "</font></center></p>" 
     1772FEET_1 = \ 
     1773""" 
     1774<p class=MsoNormal>&nbsp;</p> 
     1775<br> 
     1776<p class=MsoNormal><b><span ><center> <font size='4' > Graph 
     1777</font></span></center></b></p> 
     1778<p class=MsoNormal>&nbsp;</p> 
     1779<center> 
     1780<br><font size='4' >Model Computation</font> 
     1781<br><font size='4' >Data: "%s"</font><br> 
     1782""" 
     1783FEET_2 = \ 
     1784""" 
     1785<img src="%s" > 
     1786</img> 
     1787""" 
     1788FEET_3 = \ 
     1789""" 
     1790</center> 
     1791</div> 
     1792</body> 
     1793</html> 
     1794""" 
     1795ELINE = "<p class=MsoNormal>&nbsp;</p>" 

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

    r998ca90 ra28e52b  
    10931093                sim_page.constraints_list[index][3].SetValue(constraint_value) 
    10941094                sim_page._on_add_constraint(None) 
     1095                sim_page._manager.sim_page = sim_page 
    10951096 
    10961097    def _format_id(self, original_id): 
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