Changeset 840ac87 in sasview for src

Timestamp:

Sep 20, 2018 12:44:12 PM (6 years ago)

Author:

Paul Kienzle <pkienzle@…>

Branches:

ticket-1094-headless

Children:

1dc134e6

Parents:

a072198 (diff), 912e645 (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 ticket-1094-headless

Location:

src/sas

Files:

• sascalc/dataloader/readers/abs_reader.py (modified) (1 diff)
• sascalc/fit/pagestate.py (modified) (5 diffs)
• sasgui/guiframe/config.py (modified) (3 diffs)
• sasgui/guiframe/gui_manager.py (modified) (4 diffs)
• sasgui/guiframe/local_perspectives/plotting/parameters_panel_slicer.py (modified) (2 diffs)
• sasgui/guiframe/media/graph_help.rst (modified) (3 diffs)
• sasgui/guiframe/report_dialog.py (modified) (6 diffs)
• sasgui/guiframe/report_image_handler.py (added)
• sasgui/perspectives/calculator/media/slit_calculator_help.rst (modified) (2 diffs)
• sasgui/perspectives/calculator/model_editor.py (modified) (12 diffs)
• sasgui/perspectives/calculator/pyconsole.py (modified) (2 diffs)
• sasgui/perspectives/calculator/resolution_calculator_panel.py (modified) (1 diff)
• sasgui/perspectives/calculator/slit_length_calculator_panel.py (modified) (1 diff)
• sasgui/perspectives/fitting/basepage.py (modified) (8 diffs)
• sasgui/perspectives/fitting/fitpage.py (modified) (3 diffs)
• sasgui/perspectives/fitting/gpu_options.py (modified) (1 diff)
• sasgui/perspectives/fitting/media/fitting_help.rst (modified) (2 diffs)
• sasgui/perspectives/fitting/report_dialog.py (modified) (1 diff)
• sasgui/perspectives/invariant/invariant_panel.py (modified) (2 diffs)
• sasgui/perspectives/invariant/invariant_state.py (modified) (2 diffs)
• sasgui/perspectives/invariant/report_dialog.py (modified) (1 diff)
• sasview/local_config.py (modified) (3 diffs)
• sasview/media/.gitignore (added)
• sasview/media/README.txt (modified) (1 diff)
• sasview/media/Tutorial.pdf (modified) (previous)
• sasview/media/basic_1d_fitting_in_sasview_v3x_4x.pdf (added)
• sasview/media/simultaneous_1d_fitting_in_sasview_v3x_4x.pdf (added)
• sasview/sasview.py (modified) (2 diffs)
• sasview/test/1d_data/ISIS_Polymer_Blend_RT2.xml (added)
• sasview/test/1d_data/Ludox_silica.xml (added)
• sascalc/fit/BumpsFitting.py (modified) (5 diffs)
• sascalc/fit/fitstate.py (added)

src/sas/sascalc/dataloader/readers/abs_reader.py

@@ -171 +171 @@
 
                 try:
-                    _x = float(toks[0])
+                    _x = float(toks[4])
                     _y = float(toks[1])
                     _dy = float(toks[2])

src/sas/sascalc/fit/pagestate.py

@@ -144 +144 @@
 ################################################################################
 import time
+import re
 import os
 import sys
@@ -773 +774 @@
                     name = value.split(':', 1)[1].strip()
                     file_value = "File name:" + name
+                    #Truncating string so print doesn't complain of being outside margins
+                    if sys.platform != "win32":
+                        MAX_STRING_LENGHT = 50
+                        if len(file_value) > MAX_STRING_LENGHT:
+                            file_value = "File name:.."+file_value[-MAX_STRING_LENGHT+10:]
                     file_name = CENTRE % file_value
                     if len(title) == 0:
@@ -848 +854 @@
         html_str, text_str, title = self._get_report_string()
         # Allow 2 figures to append
-        image_links = [FEET_2%fig for fig in fig_urls]
-
+        #Constraining image width for OSX and linux, so print doesn't complain of being outside margins
+        if sys.platform == "win32":
+            image_links = [FEET_2%fig for fig in fig_urls]
+        else:
+            image_links = [FEET_2_unix%fig for fig in fig_urls]
         # final report html strings
         report_str = html_str + ELINE.join(image_links)
-
+        report_str += FEET_3
         return report_str, text_str
 
@@ -1081 +1090 @@
         if node.get('version'):
             # Get the version for model conversion purposes
-            self.version = tuple(int(e) for e in
-                                 str.split(node.get('version'), "."))
+            x = re.sub('[^\d.]', '', node.get('version'))
+            self.version = tuple(int(e) for e in str.split(x, "."))
             # The tuple must be at least 3 items long
             while len(self.version) < 3:
@@ -1495 +1504 @@
 """
 FEET_2 = \
-"""<img src="%s" ></img>
+"""<img src="%s"></img>
+"""
+FEET_2_unix = \
+"""<img src="%s" width="540"></img>
 """
 FEET_3 = \

src/sas/sasgui/guiframe/config.py

@@ -33 +33 @@
 _do_aboutbox = True
 _do_acknowledge = True
+_do_release = True
 _do_tutorial = True
 _acknowledgement_preamble =\
@@ -49 +50 @@
 _acknowledgement_citation = \
 '''M. Doucet et al. SasView Version 4.1.2, Zenodo, 10.5281/zenodo.825675'''
-
 _acknowledgement =  \
 '''This work was originally developed as part of the DANSE project funded by the US NSF under Award DMR-0520547,\n but is currently maintained by a collaboration between UTK, UMD, NIST, ORNL, ISIS, ESS, ILL, ANSTO, TU Delft, DLS, and the scattering community.\n\n SasView also contains code developed with funding from the EU Horizon 2020 programme under the SINE2020 project (Grant No 654000).\nA list of individual contributors can be found at: http://www.sasview.org/contact.html
@@ -94 +94 @@
 _corner_image = os.path.join(icon_path, "angles_flat.png")
 _welcome_image = os.path.join(icon_path, "SVwelcome.png")
-_copyright = "(c) 2009 - 2017, UTK, UMD, NIST, ORNL, ISIS, ESS, ILL, ANSTO, TU Delft, and DLS"
+_copyright = "(c) 2009 - 2018, UTK, UMD, NIST, ORNL, ISIS, ESS, ILL, ANSTO, TU Delft, and DLS"
 marketplace_url = "http://marketplace.sasview.org/"
 

src/sas/sasgui/guiframe/gui_manager.py

@@ -1276 +1276 @@
 
         wx_id = wx.NewId()
-        self._help_menu.Append(wx_id, '&Documentation', '')
+        self._help_menu.Append(wx_id, '&Documentation', 'Help documentation for SasView')
         wx.EVT_MENU(self, wx_id, self._onSphinxDocs)
 
         if config._do_tutorial and (IS_WIN or sys.platform == 'darwin'):
             wx_id = wx.NewId()
-            self._help_menu.Append(wx_id, '&Tutorial', 'Software tutorial')
+            # Pluralised both occurences of 'Tutorial' in the line below
+            # S King, Sep 2018
+            self._help_menu.Append(wx_id, '&Tutorials', 'Tutorials on how to use SasView')
             wx.EVT_MENU(self, wx_id, self._onTutorial)
+
+        if config.marketplace_url:
+            wx_id = wx.NewId()
+            self._help_menu.Append(wx_id, '&Model marketplace', 'Plug-in fitting models for SasView')
+            wx.EVT_MENU(self, wx_id, self._on_marketplace_click)
+
+        if config._do_release:
+            wx_id = wx.NewId()
+            self._help_menu.Append(wx_id, '&Release notes',
+                                   'SasView release notes and known issues')
+            wx.EVT_MENU(self, wx_id, self._onRelease)
 
         if config._do_acknowledge:
@@ -1293 +1306 @@
             logger.info("Doing help menu")
             wx_id = wx.NewId()
-            self._help_menu.Append(wx_id, '&About', 'Software information')
+            self._help_menu.Append(wx_id, '&About', 'Information about SasView')
             wx.EVT_MENU(self, wx_id, self._onAbout)
-
-        if config.marketplace_url:
-            wx_id = wx.NewId()
-            self._help_menu.Append(wx_id, '&Model marketplace', '')
-            wx.EVT_MENU(self, wx_id, self._on_marketplace_click)
 
         # Checking for updates
@@ -2137 +2145 @@
             dialog.ShowModal()
 
+    def _onRelease(self, evt):
+        """
+        Pop up the release notes
+
+        :param evt: menu event
+
+        """
+        # S King, Sep 2018
+
+        from documentation_window import DocumentationWindow
+        _TreeLocation = "user/release.html"
+        DocumentationWindow(self, -1, _TreeLocation, "",
+                            "SasView Documentation")
+
     def _onTutorial(self, evt):
         """
@@ -2144 +2166 @@
 
         """
-        if config._do_tutorial:
-            path = config.TUTORIAL_PATH
-            if IS_WIN:
-                try:
-                    from sas.sasgui.guiframe.pdfview import PDFFrame
-                    dialog = PDFFrame(None, -1, "Tutorial", path)
-                    # put icon
-                    self.put_icon(dialog)
-                    dialog.Show(True)
-                except:
-                    logger.error("Error in _onTutorial: %s" % sys.exc_value)
-                    try:
-                        # Try an alternate method
-                        logger.error(
-                            "Could not open the tutorial pdf, trying xhtml2pdf")
-                        from xhtml2pdf import pisa
-                        pisa.startViewer(path)
-                    except:
-                        logger.error(
-                            "Could not open the tutorial pdf with xhtml2pdf")
-                        msg = "This feature requires 'PDF Viewer'\n"
-                        wx.MessageBox(msg, 'Error')
-            else:
-                try:
-                    command = "open '%s'" % path
-                    os.system(command)
-                except:
-                    try:
-                        # Try an alternate method
-                        logger.error(
-                            "Could not open the tutorial pdf, trying xhtml2pdf")
-                        from xhtml2pdf import pisa
-                        pisa.startViewer(path)
-                    except:
-                        logger.error(
-                            "Could not open the tutorial pdf with xhtml2pdf")
-                        msg = "This feature requires the Preview application\n"
-                        wx.MessageBox(msg, 'Error')
+        # Action changed from that in 2.x/3.x/4.0.x/4.1.x
+        # Help >> Tutorial used to bring up a pdf of the
+        # original 2.x tutorial.
+        # Code below, implemented from 4.2.0, redirects
+        # action to the Tutorials page of the help 
+        # documentation to give access to all available
+        # tutorials
+        # S King, Sep 2018
+
+        from documentation_window import DocumentationWindow
+        _TreeLocation = "user/tutorial.html"
+        DocumentationWindow(self, -1, _TreeLocation, "",
+                            "SasView Documentation")
 
     def _onSphinxDocs(self, evt):

src/sas/sasgui/guiframe/local_perspectives/plotting/parameters_panel_slicer.py

@@ -251 +251 @@
             self.bck.Add(self.batch_slicer_button, (iy, ix), (1, 1),
                          wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
+            # Help button
+
+            self.bt_help = wx.Button(self, wx.NewId(), "HELP")
+            self.bt_help.SetToolTipString(
+                "Help for the slicer parameters and batch slicing.")
+            self.bck.Add(self.bt_help, (iy, 1), (1, 1),
+                         wx.ALIGN_RIGHT | wx.ADJUST_MINSIZE, 15)
+            wx.EVT_BUTTON(self, self.bt_help.GetId(), self.on_help)
+
             iy += 1
             self.bck.Add((5, 5), (iy, ix), (1, 1),
                          wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 5)
+
         self.bck.Layout()
         self.bck.Fit(self)
@@ -535 +545 @@
             self.default_value += "_{0}".format(key).split(" [")[0]
             self.default_value += "-{:.2f}".format(params[key])
+
+    def on_help(self, event=None):
+        """
+        Opens a help window for the slicer parameters/batch slicing window
+        :param event:
+        :return:
+        """
+        from sas.sasgui.guiframe.documentation_window import DocumentationWindow
+
+        _TreeLocation = "user/sasgui/guiframe/graph_help.html"
+        _doc_viewer = DocumentationWindow(self, wx.ID_ANY, _TreeLocation,
+                                          "#d-data-averaging",
+                                          "Data Explorer Help")

src/sas/sasgui/guiframe/media/graph_help.rst

@@ -266 +266 @@
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+.. _d_data_averaging:
 
 2D data averaging
@@ -301 +302 @@
 Alternatively, once a 'slicer' is active you can also select the region to
 average by bringing back the *Dataset Menu* and selecting *Edit Slicer
-Parameters*. A dialog window will appear in which you can enter values to
-define a region or select the number of points to plot (*nbins*).
+Parameters and Batch Fitting*. A dialog window will appear in which you can
+enter values to define a region, select the number of points to plot (*nbins*),
+or apply the slicer to any or all other 2D data plots.
 
 A separate plot window will also have appeared, displaying the requested
@@ -315 +317 @@
 
 To remove a 'slicer', bring back the *Dataset menu* and select *Clear Slicer*.
+
+Batch Slicing
+^^^^^^^^^^^^^
+
+A slicer can be applied to any or all existing 2D data plots using the 'Slicer
+Parameters' window. To open the window, select *Edit Slicer Parameters and Batch
+Fitting* in the *Dataset Menu* (see Invoking_the_dataset_menu_). Batch slicing
+options are available at the bottom of the window.
+
+Select the 2D plots you want to apply the slicer to. All 2D plots are selected
+by default. The resulting 1D data for all slicers can be saved as a text file
+and then sent to fitting by selecting the *Auto save generated 1D* check box.
+Sending data to the fitting perspective requires the data be saved.
+
+Once the auto save check box is selected, you can select where the files are
+saved. The file name for the saved data is the slicer name plus the file name
+of the original data set, plus what is in the *Append to file name* field. The
+default value in the append to field includes the names and values for all of
+the slicer parameters.
+
+The batch of slices can be sent to fitting if desired, with three options
+available. The first is to not fit the data, the second is to send the
+slices to individual fit pages, and the third is to send all sliced data to a
+single batch fit window.
+
+Clicking *Apply Slicer to Selected Plots* will create a slicer for each selected
+plot with the parameters entered in the 'Slicer Parameters' window. Depending on
+the options selected the data may then be saved, loaded as separate data sets in
+the data manager panel, and finally sent to fitting.
 
 Unmasked circular average

src/sas/sasgui/guiframe/report_dialog.py

@@ -7 +7 @@
 import sys
 import wx.html as html
+from sas.sasgui.guiframe.report_image_handler import ReportImageHandler
 
 logger = logging.getLogger(__name__)
@@ -27 +28 @@
 class BaseReportDialog(wx.Dialog):
 
-    def __init__(self, report_list, *args, **kwds):
+    def __init__(self, report_list, imgRAM, fig_urls, *args, **kwds):
         """
         Initialization. The parameters added to Dialog are:
@@ -37 +38 @@
         kwds["image"] = 'Dynamic Image'
 
+        #MemoryFSHandle for storing images
+        self.imgRAM = imgRAM
+        #Images location in urls
+        self.fig_urls = fig_urls
         # title
         self.SetTitle("Report")
@@ -66 +71 @@
         button_close = wx.Button(self, wx.ID_OK, "Close")
         button_close.SetToolTipString("Close this report window.")
+        button_close.Bind(wx.EVT_BUTTON, self.onClose,
+                          id=button_close.GetId())
         hbox.Add(button_close)
         button_close.SetFocus()
@@ -75 +82 @@
         hbox.Add(button_print)
 
-        button_save = wx.Button(self, wx.NewId(), "Save")
-        button_save.SetToolTipString("Save this report.")
-        button_save.Bind(wx.EVT_BUTTON, self.onSave, id=button_save.GetId())
-        hbox.Add(button_save)
+        if sys.platform != "darwin":
+            button_save = wx.Button(self, wx.NewId(), "Save")
+            button_save.SetToolTipString("Save this report.")
+            button_save.Bind(wx.EVT_BUTTON, self.onSave, id=button_save.GetId())
+            hbox.Add(button_save)
 
         # panel for report page
@@ -111 +119 @@
         printh.PrintText(self.report_html)
 
-    def OnClose(self, event=None):
+
+    def onClose(self, event=None):
         """
         Close the Dialog
         : event: Close button event
         """
-        self.Close()
+        for fig in self.fig_urls:
+            ReportImageHandler.remove_figure(fig)
+
+        self.Destroy()
 
     def HTML2PDF(self, data, filename):

src/sas/sasgui/perspectives/calculator/media/slit_calculator_help.rst

@@ -11 +11 @@
 -----------
 
-This tool enables X-ray users to calculate the slit size (FWHM/2) for smearing
-based on their half beam profile data.
+This tool enables X-ray users to calculate the slit size (FWHM/2) for resolution 
+smearing purposes based on their half beam profile data (as Q vs Intensity; any 
+other data fields are ignored).
 
-*NOTE! Whilst it may have some more generic applicability, the calculator has
-only been tested with beam profile data from Anton-Paar SAXSess:sup:`TM` software.*
+Method
+------
+
+The tool works by sequentially summing 10 or more intensity values until a 
+maximum value is attained. It then locates the Q values for the points just before, 
+and just after, **half** of this maximum value and interpolates between them to get 
+an accurate value for the Q value for the half maximum.
+
+NOTE! Whilst it may have some more generic applicability, the calculator has
+only been tested with beam profile data from Anton-Paar SAXSess\ :sup:`TM`\  software.
+The beam profile file does not carry any information about the units of the 
+Q data. It is probably |nm^-1| but the resolution calculations assume the slit 
+height/width has units of |Ang^-1|. If the beam profile data is not in these 
+units then it, or the result, must be manually converted.
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
@@ -27 +40 @@
 
    *NOTE! To see an example of the beam profile file format, visit the file
-   beam profile.DAT in your {installation_directory}/SasView/test folder.*
+   beam profile.DAT in your {installation_directory}/SasView/test_1d folder.*
 
 3) Once a data is loaded, the slit size is automatically computed and displayed
    in the tool window.
 
-*NOTE! The beam profile file does not carry any information about the units of
-the Q data. This calculator assumes the data has units of 1/\ |Ang|\ . If the
-data is not in these units it must be manually converted beforehand.*
-
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
 
-.. note::  This help document was last changed by Steve King, 01May2015
+.. note::  This help document was last changed by Steve King, 09Sep2018

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

@@ -43 +43 @@
 if sys.platform.count("win32") > 0:
     FONT_VARIANT = 0
-    PNL_WIDTH = 450
+    PNL_WIDTH = 500
     PNL_HEIGHT = 320
 else:
     FONT_VARIANT = 1
-    PNL_WIDTH = 590
+    PNL_WIDTH = 500
     PNL_HEIGHT = 350
 M_NAME = 'Model'
@@ -495 +495 @@
         Choose the equation to use depending on whether we now have
         a sum or multiply model then create the appropriate string
+        
+        for the sum model the result will be:
+        scale_factor * (scale1 * model_1 + scale2 * model_2) + background
+        while for the multiply model it will just be:
+        scale_factor * (model_1* model_2) + background
         """
         name = ''
         if operator == '*':
             name = 'Multi'
-            factor = 'background'
+            factor_1 = ''
+            factor_2 = ''
         else:
             name = 'Sum'
-            factor = 'scale_factor'
+            factor_1 = 'scale_1 * '
+            factor_2 = 'scale_2 * '
 
         self._operator = operator
-        self.explanation = ("  Plugin_model = scale_factor * (model_1 {} "
-            "model_2) + background").format(operator)
+        self.explanation = ("  Plugin_model = scale_factor * ({}model_1 {} "
+            "{}model_2) + background").format(factor_1,operator,factor_2)
         self.explanationctr.SetLabel(self.explanation)
         self.name = name + M_NAME
@@ -663 +670 @@
         Do the layout for parameter related widgets
         """
-        param_txt = wx.StaticText(self, -1, 'Fit Parameters NOT requiring' + \
-                                  ' polydispersity (if any): ')
-
-        param_tip = "#Set the parameters NOT requiring polydispersity " + \
-        "and their initial values.\n"
+        param_txt = wx.StaticText(self, -1, 'Fit Parameters: ')
+
+        param_tip = "#Set the parameters and their initial values.\n"
         param_tip += "#Example:\n"
         param_tip += "A = 1\nB = 1"
@@ -681 +686 @@
                                   (self.param_tcl, 1, wx.EXPAND | wx.ALL, 10)])
 
-        # Parameters with polydispersity
-        pd_param_txt = wx.StaticText(self, -1, 'Fit Parameters requiring ' + \
-                                     'polydispersity (if any): ')
-
-        pd_param_tip = "#Set the parameters requiring polydispersity and " + \
-        "their initial values.\n"
-        pd_param_tip += "#Example:\n"
-        pd_param_tip += "C = 2\nD = 2"
-        newid = wx.NewId()
-        self.pd_param_tcl = EditWindow(self, newid, wx.DefaultPosition,
-                                    wx.DefaultSize,
-                                    wx.CLIP_CHILDREN | wx.SUNKEN_BORDER)
-        self.pd_param_tcl.setDisplayLineNumbers(True)
-        self.pd_param_tcl.SetToolTipString(pd_param_tip)
-
-        self.param_sizer.AddMany([(pd_param_txt, 0, wx.LEFT, 10),
-                                  (self.pd_param_tcl, 1, wx.EXPAND | wx.ALL, 10)])
 
     def _layout_function(self):
@@ -899 +887 @@
             description = self.desc_tcl.GetValue()
             param_str = self.param_tcl.GetText()
-            pd_param_str = self.pd_param_tcl.GetText()
             func_str = self.function_tcl.GetText()
             # No input for the model function
@@ -905 +892 @@
                 if func_str.count('return') > 0:
                     self.write_file(self.fname, name, description, param_str,
-                                    pd_param_str, func_str)
+                                    func_str)
                     try:
                         result, msg = check_model(self.fname), None
@@ -945 +932 @@
         self.warning = msg
 
-    def write_file(self, fname, name, desc_str, param_str, pd_param_str, func_str):
+    def write_file(self, fname, name, desc_str, param_str, func_str):
         """
         Write content in file
@@ -952 +939 @@
         :param desc_str: content of the description strings
         :param param_str: content of params; Strings
-        :param pd_param_str: content of params requiring polydispersity; Strings
         :param func_str: content of func; Strings
         """
@@ -966 +952 @@
         # Write out parameters
         param_names = []    # to store parameter names
-        pd_params = []
         out_f.write('parameters = [ \n')
         out_f.write('#   ["name", "units", default, [lower, upper], "type", "description"],\n')
@@ -973 +958 @@
             out_f.write("    ['%s', '', %s, [-inf, inf], '', '%s'],\n"
                         % (pname, pvalue, desc))
-        for pname, pvalue, desc in self.get_param_helper(pd_param_str):
-            param_names.append(pname)
-            pd_params.append(pname)
-            out_f.write("    ['%s', '', %s, [-inf, inf], 'volume', '%s'],\n"
-                        % (pname, pvalue, desc))
         out_f.write('    ]\n')
 
         # Write out function definition
+        out_f.write('\n')
         out_f.write('def Iq(%s):\n' % ', '.join(['x'] + param_names))
         out_f.write('    """Absolute scattering"""\n')
@@ -990 +971 @@
             out_f.write('    import numpy as np')
         for func_line in func_str.split('\n'):
-            out_f.write('%s%s\n' % (spaces4, func_line))
+            out_f.write('%s%s\n' % ('    ', func_line))
         out_f.write('## uncomment the following if Iq works for vector x\n')
         out_f.write('#Iq.vectorized = True\n')
-
-        # If polydisperse, create place holders for form_volume, ER and VR
-        if pd_params:
-            out_f.write('\n')
-            out_f.write(CUSTOM_TEMPLATE_PD % {'args': ', '.join(pd_params)})
 
         # Create place holder for Iqxy
@@ -1128 +1104 @@
 description = """%(description)s"""
 
-'''
-
-CUSTOM_TEMPLATE_PD = '''\
-def form_volume(%(args)s):
-    """
-    Volume of the particles used to compute absolute scattering intensity
-    and to weight polydisperse parameter contributions.
-    """
-    return 0.0
-
-def ER(%(args)s):
-    """
-    Effective radius of particles to be used when computing structure factors.
-
-    Input parameters are vectors ranging over the mesh of polydispersity values.
-    """
-    return 0.0
-
-def VR(%(args)s):
-    """
-    Volume ratio of particles to be used when computing structure factors.
-
-    Input parameters are vectors ranging over the mesh of polydispersity values.
-    """
-    return 1.0
 '''
 

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

@@ -28 +28 @@
     Check that the model on the path can run.
     """
+    # TODO: fix model caching
+    # model_test.run_one() is directly forcing a reload of the module, but
+    # sasview_model is caching models that have already been loaded.
+    # If the sasview load happens before the test, then the module is
+    # reloaded out from under it, which causes the global variables in
+    # the model function definitions to be cleared (at least in python 2.7).
+    # To fix the proximal problem of models failing on test, perform the
+    # run_one() tests first.  To fix the deeper problem we should either
+    # remove caching from sasmodels.sasview_model.load_custom_model() or
+    # add caching to sasmodels.custom.load_custom_kernel_module().  Another
+    # option is to add a runTests method to SasviewModel which runs the
+    # test suite directly from the model info structure.  Probably some
+    # combination of options:
+    #    (1) have this function (check_model) operate on a loaded model
+    #    so that caching isn't needed in sasview_models.load_custom_model
+    #    (2) add the runTests method to SasviewModel so that tests can
+    #    be run on a loaded module.
+    #
+    # Also, note that the model test suite runs the equivalent of the
+    # "try running the model" block below, and doesn't need to be run
+    # twice.  The reason for duplicating the block here is to generate
+    # an exception that show_model_output can catch.  Need to write the
+    # runTests method so that it returns success flag as well as output
+    # string so that the extra test is not necessary.
+
+    # check the model's unit tests run
+    from sasmodels.model_test import run_one
+    result = run_one(path)
+
+    # remove cached version of the model, if any
+    from sasmodels import sasview_model
+    sasview_model.MODEL_BY_PATH.pop(path, None)
+
     # try running the model
-    from sasmodels.sasview_model import load_custom_model
-    Model = load_custom_model(path)
+    Model = sasview_model.load_custom_model(path)
     model = Model()
     q =  np.array([0.01, 0.1])
@@ -36 +68 @@
     qx, qy =  np.array([0.01, 0.01]), np.array([0.1, 0.1])
     Iqxy = model.evalDistribution([qx, qy])
-
-    # check the model's unit tests run
-    from sasmodels.model_test import run_one
-    result = run_one(path)
 
     return result

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

@@ -18 +18 @@
 matplotlib.use('WXAgg')
 from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
-from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
+from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg as Toolbar
 from matplotlib.backend_bases import FigureManagerBase
 # Wx-Pylab magic for displaying plots within an application's window.

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

@@ -248 +248 @@
             Complete the loading and compute the slit size
         """
+        if isinstance(data, list):
+            data = data[0]
         if data is None or data.__class__.__name__ == 'Data2D':
             if self.parent.parent is None:

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

@@ -31 +31 @@
 
 from sas.sasgui.guiframe.panel_base import PanelBase
+from sas.sasgui.guiframe.report_image_handler import ReportImageHandler
 from sas.sasgui.guiframe.utils import format_number, check_float, IdList, \
     check_int
@@ -641 +642 @@
         # get the strings for report
         report_str, text_str = self.state.report(fig_urls=refs)
-
         # Show the dialog
         report_list = [report_str, text_str, images]
-        dialog = ReportDialog(report_list, None, wx.ID_ANY, "")
+        dialog = ReportDialog(report_list, imgRAM, refs, None, wx.ID_ANY, "")
         dialog.Show()
 
@@ -652 +652 @@
         by plotting, putting it into wx.FileSystem image object
         """
-        images = []
-        refs = []
-
-        # For no figures in the list, prepare empty plot
-        if figs is None or len(figs) == 0:
-            figs = [None]
-
-        # Loop over the list of figures
-        # use wx.MemoryFSHandler
-        imgRAM = wx.MemoryFSHandler()
-        for fig in figs:
-            if fig is not None:
-                ind = figs.index(fig)
-                canvas = canvases[ind]
-
-            # store the image in wx.FileSystem Object
-            wx.FileSystem.AddHandler(wx.MemoryFSHandler())
-
-            # index of the fig
-            ind = figs.index(fig)
-
-            # AddFile, image can be retrieved with 'memory:filename'
-            name = 'img_fit%s.png' % ind
-            refs.append('memory:' + name)
-            imgRAM.AddFile(name, canvas.bitmap, wx.BITMAP_TYPE_PNG)
-
-            # append figs
-            images.append(fig)
-
-        return imgRAM, images, refs
-
+        bitmaps = []
+        for canvas in canvases:
+            bitmaps.append(canvas.bitmap)
+        imgs, refs = ReportImageHandler.set_figs(figs, bitmaps, 'fit')
+
+        return ReportImageHandler.instance, imgs, refs
 
     def on_save(self, event):
@@ -1472 +1447 @@
             # we need to check here ourselves.
             if not is_modified:
-                is_modified = (self._check_value_enter(self.fittable_param)
-                               or self._check_value_enter(self.fixed_param)
-                               or self._check_value_enter(self.parameters))
+                is_modified = self._check_value_enter(self.fittable_param)
+                is_modified = self._check_value_enter(
+                    self.fixed_param) or is_modified
+                is_modified = self._check_value_enter(
+                    self.parameters) or is_modified
 
             # Here we should check whether the boundaries have been modified.
@@ -1536 +1513 @@
                         data=[self.data])
             # Check the values
-            is_modified = (self._check_value_enter(self.fittable_param)
-                           or self._check_value_enter(self.fixed_param)
-                           or self._check_value_enter(self.parameters))
+            is_modified = self._check_value_enter(self.fittable_param)
+            is_modified = self._check_value_enter(self.fixed_param) or is_modified
+            is_modified = self._check_value_enter(self.parameters) or is_modified
 
             # If qmin and qmax have been modified, update qmin and qmax and
@@ -2324 +2301 @@
 
             # Update value in model if it has changed
-            if value != self.model.getParam(name):
+            if (value != self.model.getParam(name) or
+                    (np.isnan(value) and np.isnan(self.model.getParam(name)))):
                 self.model.setParam(name, value)
                 is_modified = True
@@ -2551 +2529 @@
             # draw
             self._draw_model()
+            self.Layout()
             self.Refresh()
         except Exception:
@@ -2799 +2778 @@
         Function called when 'Help' button is pressed next to model
         of interest.  This calls DocumentationWindow from
-        documentation_window.py. It will load the top level of the model
-        help documenation sphinx generated html if no model is presented.
-        If a model IS present then if documention for that model exists
-        it will load to that  point otherwise again it will go to the top.
-        For Wx2.8 and below is used (i.e. non-released through installer)
-        a browser is loaded and the top of the model documentation only is
-        accessible because webbrowser module does not pass anything after
-        the # to the browser.
+        documentation_window.py. It will load the top level of the html model
+        help documenation sphinx generated if either a plugin model (which
+        normally does not have an html help help file) is selected or if no
+        model is selected. Otherwise, if a regula model is selected, the
+        documention for that model will be sent to a browser window.
+
+        :todo the quick fix for no documentation in plugins is the if statment.
+        However, the right way to do this would be to check whether the hmtl
+        file exists and load the model docs if it does and the general docs if
+        it doesn't - this will become important if we ever figure out how to
+        build docs for plugins on the fly.  Sep 9, 2018 -PDB
 
         :param event: on Help Button pressed event
         """
 
-        if self.model is not None:
+        if (self.model is not None) and (self.categorybox.GetValue()
+                                         != "Plugin Models"):
             name = self.formfactorbox.GetValue()
             _TreeLocation = 'user/models/%s.html' % name

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

@@ -705 +705 @@
 
                         ix = 3
-                        ctl2 = wx.TextCtrl(self, wx.ID_ANY,
-                                           size=(_BOX_WIDTH / 1.3, 20),
-                                           style=0)
+                        ctl2 = BGTextCtrl(self, wx.ID_ANY,
+                                           size=(_BOX_WIDTH / 1.3, 20))
 
                         self.sizer4_4.Add(ctl2, (iy, ix), (1, 1),
@@ -1997 +1996 @@
         self.on_smear_helper()
         self.on_set_focus(None)
+        self.Layout()
         self.Refresh()
         # update model plot with new data information
@@ -2891 +2891 @@
                         text2.Hide()
                     ix += 1
-                    ctl2 = wx.TextCtrl(self, wx.ID_ANY,
-                                       size=(_BOX_WIDTH / 1.2, 20), style=0)
+                    ctl2 = BGTextCtrl(self, wx.ID_ANY,
+                                       size=(_BOX_WIDTH / 1.2, 20))
                     sizer.Add(ctl2, (iy, ix), (1, 1),
                               wx.EXPAND | wx.ADJUST_MINSIZE, 0)

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

@@ -139 +139 @@
 
         test_text = wx.StaticText(self, -1, "WARNING: Running tests can take a few minutes!")
+        test_text2 = wx.StaticText(self, -1, "NOTE: No test will run if No OpenCL is checked")
+        test_text.SetForegroundColour(wx.RED)
+        self.vbox.Add(test_text2, 0, wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 10)
         self.vbox.Add(test_text, 0, wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 10)
 

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

@@ -180 +180 @@
 *checked*\ .
 
-Also note that the 'Fit Parameters' have been split into two sections: those
-which can be polydisperse (shape and orientation parameters) and those which are
-not (eg, scattering length densities).
-
 A model file generated by this option can be viewed and further modified using
 the :ref:`Advanced_Plugin_Editor` .
 
-**SasView version 4.2** made it possible to specify whether a plugin created with
-the *New Plugin Model* dialog is actually a form factor P(Q) or a structure factor
-S(Q). To do this, simply add one or other of the following lines under the *import*
-statements.
+Note that the New Plugin Model Feature currently does not allow for parameters
+to be polydisperse.  However they can be edited in the Advanced Editor.
+
+
+**SasView version 4.2** made it possible to specify whether a plugin created
+with the *New Plugin Model* dialog is actually a form factor P(Q) or a structure
+factor S(Q). To do this, simply add one or other of the following lines under
+the *import* statements.
 
 For a form factor::
@@ -200 +200 @@
      structure_factor = True
 
-If the plugin is a structure factor it is *also* necessary to add two variables to
-the parameter list::
+If the plugin is a structure factor it is *also* necessary to add two variables
+to the parameter list::
 
      parameters = [

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

@@ -72 +72 @@
         filename = basename + ext
 
-        # save figures
-        pictures = []
-        for num in range(self.nimages):
-            pic_name = basename + '_img%s.png' % num
-            # save the image for use with pdf writer
-            self.report_list[2][num].savefig(pic_name)
-            pictures.append(pic_name)
+        # save the images for use with pdf writer
+        pictures = [
+            '_'.join((basename, url.split(':')[1])) for url in self.fig_urls]
+        for i, pic in enumerate(pictures):
+            self.report_list[2][i].savefig(pic)
 
         # translate png references int html from in-memory name to on-disk name
-        html = self.report_html.replace("memory:img_fit", basename+'_img')
+        html = self.report_html.replace("memory:", basename+'_')
 
         #set file extensions

src/sas/sasgui/perspectives/invariant/invariant_panel.py

@@ -24 +24 @@
 from sas.sasgui.guiframe.panel_base import PanelBase
 from sas.sasgui.guiframe.documentation_window import DocumentationWindow
+from sas.sasgui.guiframe.report_image_handler import ReportImageHandler
 
 logger = logging.getLogger(__name__)
@@ -783 +784 @@
         report_img = self.state.image
         report_list = [report_html_str, report_text_str, report_img]
-        dialog = ReportDialog(report_list, None, -1, "")
+        ReportImageHandler.check_for_empty_instance()
+        imgRAM = ReportImageHandler.instance.img_holder
+        refs = [self.state.wximgbmp]
+        dialog = ReportDialog(report_list, imgRAM, refs, None, wx.ID_ANY, "")
         dialog.Show()
 

src/sas/sasgui/perspectives/invariant/invariant_state.py

@@ -12 +12 @@
 from lxml import etree
 from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader
+from sas.sasgui.guiframe.report_image_handler import ReportImageHandler
 from sas.sascalc.dataloader.readers.cansas_reader import get_content
 from sas.sasgui.guiframe.utils import format_number
@@ -611 +612 @@
         wximgbmp = wx.BitmapFromImage(wximg)
         # store the image in wx.FileSystem Object
-        wx.FileSystem.AddHandler(wx.MemoryFSHandler())
-        # use wx.MemoryFSHandler
-        self.imgRAM = wx.MemoryFSHandler()
-        # AddFile, image can be retrieved with 'memory:filename'
-        self.imgRAM.AddFile('img_inv.png', wximgbmp, wx.BITMAP_TYPE_PNG)
-
-        self.wximgbmp = 'memory:img_inv.png'
-        self.image = fig
+        imgs, refs = ReportImageHandler.set_figs([fig], [wximgbmp], 'inv')
+
+        self.wximgbmp = refs[0]
+        self.image = imgs[0]
 
 class Reader(CansasReader):

src/sas/sasgui/perspectives/invariant/report_dialog.py

@@ -41 +41 @@
 
         # put image path in the report string
-        self.report_html = self.report_list[0] % "memory:img_inv.png"
+        self.report_html = self.report_list[0] % self.fig_urls[0]
         # layout
         self._setup_layout()

src/sas/sasview/local_config.py

@@ -33 +33 @@
 _do_aboutbox = True
 _do_acknowledge = True
+_do_release = True
 _do_tutorial = True
 _acknowledgement_preamble =\
@@ -48 +49 @@
 '''This work benefited from the use of the SasView application, originally developed under NSF Award DMR-0520547. SasView also contains code developed with funding from the EU Horizon 2020 programme under the SINE2020 project Grant No 654000.'''
 _acknowledgement_citation = \
-'''M. Doucet et al. SasView Version 4.1.2, Zenodo, 10.5281/zenodo.825675'''
-
+'''M. Doucet et al. SasView Version 4.2, Zenodo, 10.5281/zenodo.1412041'''
 _acknowledgement =  \
 '''This work was originally developed as part of the DANSE project funded by the US NSF under Award DMR-0520547,\n but is currently maintained by a collaboration between UTK, UMD, NIST, ORNL, ISIS, ESS, ILL, ANSTO, TU Delft, DLS, and the scattering community.\n\n SasView also contains code developed with funding from the EU Horizon 2020 programme under the SINE2020 project (Grant No 654000).\nA list of individual contributors can be found at: http://www.sasview.org/contact.html
@@ -94 +94 @@
 _corner_image = os.path.join(icon_path, "angles_flat.png")
 _welcome_image = os.path.join(icon_path, "SVwelcome.png")
-_copyright = "(c) 2009 - 2017, UTK, UMD, NIST, ORNL, ISIS, ESS, ILL, ANSTO, TU Delft, and DLS"
+_copyright = "(c) 2009 - 2018, UTK, UMD, NIST, ORNL, ISIS, ESS, ILL, ANSTO, TU Delft, and DLS"
 marketplace_url = "http://marketplace.sasview.org/"
 

src/sas/sasview/media/README.txt

@@ +1 @@
+The files in this folder are what get shipped in the installer \media folder.
+
+The help documentation gets shipped in the /doc folder.
+
 This Tutorial.pdf is what appears when you click on 'Tutorial' under 'Help'
-in the menu bar.
+in the SasView menu bar. It has been manually copied over from sasview/docs/sasview.
 
-The source files are in: /sasview/docs/sasview
-
-The getting_started_with_sasview.pdf has been manually added here until the auto-generated LibreOffice doc build is up and running.
+The new tutorial pdfs here have been manually copied over from the website /downloads folder.

src/sas/sasview/sasview.py

@@ -43 +43 @@
         from sas.sasgui.guiframe.gui_manager import SasViewApp
         self.gui = SasViewApp(0)
+        if sys.platform == "darwin":
+            self.check_sasmodels_compiler()
         # Set the application manager for the GUI
         self.gui.set_manager(self)
@@ -130 +132 @@
         self.gui.MainLoop()
 
+    def check_sasmodels_compiler(self):
+        """
+        Checking c compiler for sasmodels and raises xcode command line
+        tools for installation
+        """
+        #wx should be importable at this stage
+        import wx
+        import subprocess
+        #Generic message box created becuase standard MessageBox is not moveable
+        class GenericMessageBox(wx.Dialog):
+            def __init__(self, parent, text, title = ''):
+
+                wx.Dialog.__init__(self, parent, -1, title = title,
+                               size = (360,200), pos=(20,60),
+                               style = wx.STAY_ON_TOP | wx.DEFAULT_DIALOG_STYLE)
+                panel = wx.Panel(self, -1)
+                top_row_sizer = wx.BoxSizer(wx.HORIZONTAL)
+
+                error_bitmap = wx.ArtProvider.GetBitmap(
+                    wx.ART_ERROR, wx.ART_MESSAGE_BOX
+                )
+                error_bitmap_ctrl = wx.StaticBitmap(panel, -1)
+                error_bitmap_ctrl.SetBitmap(error_bitmap)
+                label = wx.StaticText(panel, -1, text)
+                top_row_sizer.Add(error_bitmap_ctrl, flag=wx.ALL, border=10)
+                top_row_sizer.Add(label, flag=wx.ALIGN_CENTER_VERTICAL)
+
+                #Create the OK button in the bottom row.
+                ok_button = wx.Button(panel, wx.ID_OK )
+                self.Bind(wx.EVT_BUTTON, self.on_ok, source=ok_button)
+                ok_button.SetFocus()
+                ok_button.SetDefault()
+
+                sizer = wx.BoxSizer(wx.VERTICAL)
+                sizer.Add(top_row_sizer)
+                sizer.Add(ok_button, flag=wx.ALIGN_CENTER | wx.ALL, border=5)
+                panel.SetSizer(sizer)
+
+            def on_ok(self, event):
+                self.Destroy()
+
+        logger = logging.getLogger(__name__)
+        try:
+            subprocess.check_output(["cc","--version"], stderr=subprocess.STDOUT)
+        except subprocess.CalledProcessError as exc:
+            dlg = GenericMessageBox(parent=None,
+            text='No compiler installed. Please install command line\n'
+                'developers tools by clicking \"Install\" in another winodw\n\n'
+                'Alternatively click \"Not Now\" and use OpenCL\n'
+                 'compiler, which can be set up from menu Fitting->OpenCL Options\n\n',
+            title = 'Compiler Info')
+            dlg.Show()
+            logger.error("No compiler installed. %s\n"%(exc))
+            logger.error(traceback.format_exc())
 
 def setup_logging():

src/sas/sascalc/fit/BumpsFitting.py

@@ -2 +2 @@
 BumpsFitting module runs the bumps optimizer.
 """
+from __future__ import print_function
+
 import os
 from datetime import timedelta, datetime
@@ -9 +11 @@
 
 from bumps import fitters
+
 try:
     from bumps.options import FIT_CONFIG
+    # Preserve bumps default fitter in case someone wants it later
+    BUMPS_DEFAULT_FITTER = FIT_CONFIG.selected_id
     # Default bumps to use the Levenberg-Marquardt optimizer
     FIT_CONFIG.selected_id = fitters.LevenbergMarquardtFit.id
@@ -17 +22 @@
 except ImportError:
     # CRUFT: Bumps changed its handling of fit options around 0.7.5.6
+    # Preserve bumps default fitter in case someone wants it later
+    BUMPS_DEFAULT_FITTER = fitters.FIT_DEFAULT
     # Default bumps to use the Levenberg-Marquardt optimizer
     fitters.FIT_DEFAULT = 'lm'
@@ -126 +133 @@
         if initial_values is not None:
             self._reset_pars(fitted, initial_values)
+        #print("constraints", constraints)
         self.constraints = dict(constraints)
         self.set_fitted(fitted)
@@ -222 +230 @@
     def _setup(self):
         exprs = {}
-        for M in self.models:
-            exprs.update((".".join((M.name, k)), v) for k, v in M.constraints.items())
+        for model in self.models:
+            exprs.update((".".join((model.name, k)), v)
+                         for k, v in model.constraints.items())
         if exprs:
-            symtab = dict((".".join((M.name, k)), p)
-                          for M in self.models
-                          for k, p in M.parameters().items())
+            symtab = dict((".".join((model.name, k)), p)
+                          for model in self.models
+                          for k, p in model.parameters().items())
             self.update = compile_constraints(symtab, exprs)
         else: