Changeset ccf58fb in sasview for src/sas/sasgui

Timestamp:

Sep 11, 2017 6:08:09 AM (7 years ago)

Author:

lewis

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, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload

Children:

0794ce3

Parents:

a309667 (diff), f9ba422 (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 corfunc3d

Location:

src/sas/sasgui

Files:

• guiframe/local_perspectives/data_loader/data_loader.py (modified) (11 diffs)
• perspectives/calculator/model_editor.py (modified) (16 diffs)
• perspectives/calculator/pyconsole.py (modified) (2 diffs)
• perspectives/file_converter/converter_panel.py (modified) (12 diffs)
• perspectives/file_converter/file_converter.py (modified) (1 diff)
• perspectives/file_converter/media/file_converter_help.rst (modified) (4 diffs)
• perspectives/fitting/fitting.py (modified) (10 diffs)
• perspectives/fitting/models.py (modified) (2 diffs)
• perspectives/pr/inversion_panel.py (modified) (12 diffs)
• perspectives/pr/inversion_state.py (modified) (6 diffs)
• perspectives/pr/media/pr_help.rst (modified) (1 diff)
• perspectives/pr/pr.py (modified) (10 diffs)
• perspectives/corfunc/corfunc.py (modified) (1 diff)
• perspectives/corfunc/corfunc_panel.py (modified) (5 diffs)
• perspectives/corfunc/corfunc_state.py (modified) (1 diff)
• perspectives/corfunc/media/corfunc_help.rst (modified) (9 diffs)
• perspectives/corfunc/plot_labels.py (modified) (1 diff)

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

@@ -11 +11 @@
 
 from sas.sascalc.dataloader.loader import Loader
+from sas.sascalc.dataloader.loader_exceptions import NoKnownLoaderException
 from sas.sasgui.guiframe.plugin_base import PluginBase
 from sas.sasgui.guiframe.events import StatusEvent
@@ -41 +42 @@
 APPLICATION_WLIST = config.APPLICATION_WLIST
 
+
 class Plugin(PluginBase):
 
@@ -56 +58 @@
         """
         # menu for data files
-        menu_list = []
         data_file_hint = "load one or more data in the application"
         menu_list = [('&Load Data File(s)', data_file_hint, self.load_data)]
         gui_style = self.parent.get_style()
         style = gui_style & GUIFRAME.MULTIPLE_APPLICATIONS
-        style1 = gui_style & GUIFRAME.DATALOADER_ON
         if style == GUIFRAME.MULTIPLE_APPLICATIONS:
             # menu for data from folder
@@ -102 +102 @@
         self.get_data(file_list)
 
-
     def can_load_data(self):
         """
@@ -108 +107 @@
         """
         return True
-
 
     def _load_folder(self, event):
@@ -140 +138 @@
         """
         if error is not None or str(error).strip() != "":
-            dial = wx.MessageDialog(self.parent, str(error), 'Error Loading File',
+            dial = wx.MessageDialog(self.parent, str(error),
+                                    'Error Loading File',
                                     wx.OK | wx.ICON_EXCLAMATION)
             dial.ShowModal()
@@ -149 +148 @@
         """
         if os.path.isdir(path):
-            return [os.path.join(os.path.abspath(path), filename) for filename in os.listdir(path)]
+            return [os.path.join(os.path.abspath(path), filename) for filename
+                    in os.listdir(path)]
 
     def _process_data_and_errors(self, item, p_file, output, message):
@@ -178 +178 @@
         for p_file in path:
             basename = os.path.basename(p_file)
+            # Skip files that start with a period
+            if basename.startswith("."):
+                msg = "The folder included a potential hidden file - %s." \
+                      % basename
+                msg += " Do you wish to load this file as data?"
+                msg_box = wx.MessageDialog(None, msg, 'Warning',
+                                           wx.OK | wx.CANCEL)
+                if msg_box.ShowModal() == wx.ID_CANCEL:
+                    continue
             _, extension = os.path.splitext(basename)
             if extension.lower() in EXTENSIONS:
@@ -213 +222 @@
                 info="info")
 
-            except:
-                logger.error(sys.exc_value)
-
-                error_message = "The Data file you selected could not be loaded.\n"
-                error_message += "Make sure the content of your file"
-                error_message += " is properly formatted.\n"
-                error_message += "When contacting the SasView team, mention the"
-                error_message += " following:\n"
-                error_message += "Error: " + str(sys.exc_info()[1])
-                file_errors[basename] = [error_message]
-                self.load_update(output=output, message=error_message, info="warning")
+            except NoKnownLoaderException as e:
+                exception_occurred = True
+                logger.error(e.message)
+
+                error_message = "Loading data failed!\n" + e.message
+                self.load_update(output=None, message=e.message, info="warning")
+
+            except Exception as e:
+                exception_occurred = True
+                logger.error(e.message)
+
+                file_err = "The Data file you selected could not be "
+                file_err += "loaded.\nMake sure the content of your file"
+                file_err += " is properly formatted.\n"
+                file_err += "When contacting the SasView team, mention the"
+                file_err += " following:\n"
+                file_err += e.message
+                file_errors[basename] = [file_err]
 
         if len(file_errors) > 0:
@@ -233 +249 @@
                     error_message += message + "\n"
                 error_message += "\n"
-            self.load_update(output=output, message=error_message, info="error")
-
-        self.load_complete(output=output, message="Loading data complete!",
-            info="info")
+            if not exception_occurred: # Some data loaded but with errors
+                self.load_update(output=output, message=error_message, info="error")
+
+        if not exception_occurred: # Everything loaded as expected
+            self.load_complete(output=output, message="Loading data complete!",
+                               info="info")
+        else:
+            self.load_complete(output=None, message=error_message, info="error")
+
 
     def load_update(self, output=None, message="", info="warning"):
@@ -245 +266 @@
             wx.PostEvent(self.parent, StatusEvent(status=message, info=info,
                                                   type="progress"))
-    def load_complete(self, output, message="", error_message="", path=None,
-                      info="warning"):
-        """
-         post message to  status bar and return list of data
-        """
-        wx.PostEvent(self.parent, StatusEvent(status=message,
-                                              info=info,
+
+    def load_complete(self, output, message="", info="warning"):
+        """
+         post message to status bar and return list of data
+        """
+        wx.PostEvent(self.parent, StatusEvent(status=message, info=info,
                                               type="stop"))
-        # if error_message != "":
-        #    self.load_error(error_message)
-        self.parent.add_data(data_list=output)
+        if output is not None:
+            self.parent.add_data(data_list=output)

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

@@ -643 +643 @@
         self.name_hsizer = None
         self.name_tcl = None
+        self.overwrite_cb = None
         self.desc_sizer = None
         self.desc_tcl = None
@@ -657 +658 @@
         self.warning = ""
         #This does not seem to be used anywhere so commenting out for now
-        #    -- PDB 2/26/17 
+        #    -- PDB 2/26/17
         #self._description = "New Plugin Model"
         self.function_tcl = None
@@ -689 +690 @@
         #title name [string]
         name_txt = wx.StaticText(self, -1, 'Function Name : ')
-        overwrite_cb = wx.CheckBox(self, -1, "Overwrite existing plugin model of this name?", (10, 10))
-        overwrite_cb.SetValue(False)
-        overwrite_cb.SetToolTipString("Overwrite it if already exists?")
-        wx.EVT_CHECKBOX(self, overwrite_cb.GetId(), self.on_over_cb)
+        self.overwrite_cb = wx.CheckBox(self, -1, "Overwrite existing plugin model of this name?", (10, 10))
+        self.overwrite_cb.SetValue(False)
+        self.overwrite_cb.SetToolTipString("Overwrite it if already exists?")
+        wx.EVT_CHECKBOX(self, self.overwrite_cb.GetId(), self.on_over_cb)
         self.name_tcl = wx.TextCtrl(self, -1, size=(PANEL_WIDTH * 3 / 5, -1))
         self.name_tcl.Bind(wx.EVT_TEXT_ENTER, self.on_change_name)
@@ -700 +701 @@
         self.name_tcl.SetToolTipString(hint_name)
         self.name_hsizer.AddMany([(self.name_tcl, 0, wx.LEFT | wx.TOP, 0),
-                                  (overwrite_cb, 0, wx.LEFT, 20)])
+                                  (self.overwrite_cb, 0, wx.LEFT, 20)])
         self.name_sizer.AddMany([(name_txt, 0, wx.LEFT | wx.TOP, 10),
                                  (self.name_hsizer, 0,
@@ -740 +741 @@
         self.param_sizer.AddMany([(param_txt, 0, wx.LEFT, 10),
                                   (self.param_tcl, 1, wx.EXPAND | wx.ALL, 10)])
-        
+
         # Parameters with polydispersity
         pd_param_txt = wx.StaticText(self, -1, 'Fit Parameters requiring ' + \
@@ -755 +756 @@
         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)])
@@ -995 +996 @@
             info = 'Error'
             color = 'red'
+            self.overwrite_cb.SetValue(True)
+            self.overwrite_name = True
         else:
             self._notes = result
@@ -1030 +1033 @@
         if has_scipy:
             lines.insert(0, 'import scipy')
-        
-        # Think about 2D later        
+
+        # Think about 2D later
         #self.is_2d = func_str.count("#self.ndim = 2")
         #line_2d = ''
         #if self.is_2d:
         #    line_2d = CUSTOM_2D_TEMP.split('\n')
-        
-        # Also think about test later        
+
+        # Also think about test later
         #line_test = TEST_TEMPLATE.split('\n')
         #local_params = ''
@@ -1043 +1046 @@
         spaces4  = ' '*4
         spaces13 = ' '*13
-        spaces16 = ' '*16     
+        spaces16 = ' '*16
         param_names = []    # to store parameter names
         has_scipy = func_str.count("scipy.")
@@ -1055 +1058 @@
             out_f.write(line + '\n')
             if line.count('#name'):
-                out_f.write('name = "%s" \n' % name)               
+                out_f.write('name = "%s" \n' % name)
             elif line.count('#title'):
-                out_f.write('title = "User model for %s"\n' % name)               
+                out_f.write('title = "User model for %s"\n' % name)
             elif line.count('#description'):
-                out_f.write('description = "%s"\n' % desc_str)               
+                out_f.write('description = "%s"\n' % desc_str)
             elif line.count('#parameters'):
                 out_f.write('parameters = [ \n')
@@ -1065 +1068 @@
                     p_line = param_line.lstrip().rstrip()
                     if p_line:
-                        pname, pvalue = self.get_param_helper(p_line)
+                        pname, pvalue, desc = self.get_param_helper(p_line)
                         param_names.append(pname)
-                        out_f.write("%s['%s', '', %s, [-numpy.inf, numpy.inf], '', ''],\n" % (spaces16, pname, pvalue))
+                        out_f.write("%s['%s', '', %s, [-numpy.inf, numpy.inf], '', '%s'],\n" % (spaces16, pname, pvalue, desc))
                 for param_line in pd_param_str.split('\n'):
                     p_line = param_line.lstrip().rstrip()
                     if p_line:
-                        pname, pvalue = self.get_param_helper(p_line)
+                        pname, pvalue, desc = self.get_param_helper(p_line)
                         param_names.append(pname)
-                        out_f.write("%s['%s', '', %s, [-numpy.inf, numpy.inf], 'volume', ''],\n" % (spaces16, pname, pvalue))
+                        out_f.write("%s['%s', '', %s, [-numpy.inf, numpy.inf], 'volume', '%s'],\n" % (spaces16, pname, pvalue, desc))
                 out_f.write('%s]\n' % spaces13)
-            
+
         # No form_volume or ER available in simple model editor
         out_f.write('def form_volume(*arg): \n')
@@ -1082 +1085 @@
         out_f.write('def ER(*arg): \n')
         out_f.write('    return 1.0 \n')
-        
+
         # function to compute
         out_f.write('\n')
@@ -1091 +1094 @@
         for func_line in func_str.split('\n'):
             out_f.write('%s%s\n' % (spaces4, func_line))
-        
+
         Iqxy_string = 'return Iq(numpy.sqrt(x**2+y**2) '
-            
+
         out_f.write('\n')
         out_f.write('def Iqxy(x, y ')
@@ -1113 +1116 @@
         items = line.split(";")
         for item in items:
-            name = item.split("=")[0].lstrip().rstrip()
+            name = item.split("=")[0].strip()
+            description = ""
             try:
-                value = item.split("=")[1].lstrip().rstrip()
+                value = item.split("=")[1].strip()
+                if value.count("#"):
+                    # If line ends in a comment, remove it before parsing float
+                    index = value.index("#")
+                    description = value[(index + 1):].strip()
+                    value = value[:value.index("#")].strip()
                 float(value)
-            except:
+            except ValueError:
                 value = 1.0 # default
 
-        return name, value
+        return name, value, description
 
     def set_function_helper(self, line):
@@ -1204 +1213 @@
 import numpy
 
-#name 
+#name
 
 #title
@@ -1210 +1219 @@
 #description
 
-#parameters 
+#parameters
 
 """

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

@@ -37 +37 @@
     Iqxy = model.evalDistribution([qx, qy])
 
-    result = """
-    Iq(%s) = %s
-    Iqxy(%s, %s) = %s
-    """%(q, Iq, qx, qy, Iqxy)
+    # check the model's unit tests run
+    from sasmodels.model_test import run_one
+    result = run_one(path)
 
     return result
@@ -89 +88 @@
         ok = wx.Button(self, wx.ID_OK, "OK")
 
-        # Mysterious constraint layouts from 
+        # Mysterious constraint layouts from
         # https://www.wxpython.org/docs/api/wx.lib.layoutf.Layoutf-class.html
         lc = layoutf.Layoutf('t=t5#1;b=t5#2;l=l5#1;r=r5#1', (self,ok))

src/sas/sasgui/perspectives/file_converter/converter_panel.py

@@ -24 +24 @@
 from sas.sascalc.file_converter.otoko_loader import OTOKOLoader
 from sas.sascalc.file_converter.bsl_loader import BSLLoader
+from sas.sascalc.file_converter.ascii2d_loader import ASCII2DLoader
 from sas.sascalc.file_converter.nxcansas_writer import NXcanSASWriter
 from sas.sascalc.dataloader.data_info import Detector
@@ -35 +36 @@
     _STATICBOX_WIDTH = 410
     _BOX_WIDTH = 200
-    PANEL_SIZE = 480
+    PANEL_SIZE = 520
     FONT_VARIANT = 0
 else:
@@ -41 +42 @@
     _STATICBOX_WIDTH = 430
     _BOX_WIDTH = 200
-    PANEL_SIZE = 500
+    PANEL_SIZE = 540
     FONT_VARIANT = 1
 
@@ -352 +353 @@
             w.write(frame_data, output_path)
 
+    def convert_2d_data(self, dataset):
+        metadata = self.get_metadata()
+        for key, value in metadata.iteritems():
+            setattr(dataset[0], key, value)
+
+        w = NXcanSASWriter()
+        w.write(dataset, self.output.GetPath())
+
     def on_convert(self, event):
         """Called when the Convert button is clicked"""
@@ -367 +376 @@
                 qdata, iqdata = self.extract_otoko_data(self.q_input.GetPath())
                 self.convert_1d_data(qdata, iqdata)
+            elif self.data_type == 'ascii2d':
+                loader = ASCII2DLoader(self.iq_input.GetPath())
+                data = loader.load()
+                dataset = [data] # ASCII 2D only ever contains 1 frame
+                self.convert_2d_data(dataset)
             else: # self.data_type == 'bsl'
                 dataset = self.extract_bsl_data(self.iq_input.GetPath())
@@ -372 +386 @@
                     # Cancelled by user
                     return
-
-                metadata = self.get_metadata()
-                for key, value in metadata.iteritems():
-                    setattr(dataset[0], key, value)
-
-                w = NXcanSASWriter()
-                w.write(dataset, self.output.GetPath())
+                self.convert_2d_data(dataset)
+
         except Exception as ex:
             msg = str(ex)
@@ -399 +408 @@
     def validate_inputs(self):
         msg = "You must select a"
-        if self.q_input.GetPath() == '' and self.data_type != 'bsl':
+        if self.q_input.GetPath() == '' and self.data_type != 'bsl' \
+            and self.data_type != 'ascii2d':
             msg += " Q Axis input file."
         elif self.iq_input.GetPath() == '':
@@ -472 +482 @@
         dtype = event.GetEventObject().GetName()
         self.data_type = dtype
-        if dtype == 'bsl':
+        if dtype == 'bsl' or dtype == 'ascii2d':
             self.q_input.SetPath("")
             self.q_input.Disable()
@@ -500 +510 @@
 
         instructions = (
-        "Select linked single column 1D ASCII files containing the Q-axis and "
-        "Intensity-axis data, or 1D BSL/OTOKO files, or a 2D BSL/OTOKO file, "
-        "then choose where to save the converted file, and click Convert.\n"
-        "1D ASCII and BSL/OTOKO files can be converted to CanSAS (XML) or "
-        "NXcanSAS (HDF5) formats. 2D BSL/OTOKO files can only be converted to "
-        "the NXcanSAS format.\n"
-        "Metadata can be optionally added for the CanSAS XML format."
+        "If converting a 1D dataset, select linked single-column ASCII files "
+        "containing the Q-axis and intensity-axis data, or a 1D BSL/OTOKO file."
+        " If converting 2D data, select an ASCII file in the ISIS 2D file "
+        "format, or a 2D BSL/OTOKO file. Choose where to save the converted "
+        "file and click convert.\n"
+        "One dimensional ASCII and BSL/OTOKO files can be converted to CanSAS "
+        "(XML) or NXcanSAS (HDF5) formats. Two dimensional datasets can only be"
+        " converted to the NXcanSAS format.\n"
+        "Metadata can also be optionally added to the output file."
         )
 
@@ -526 +538 @@
             wx.ALIGN_CENTER_VERTICAL, 5)
         radio_sizer = wx.BoxSizer(wx.HORIZONTAL)
-        ascii_btn = wx.RadioButton(self, -1, "ASCII", name="ascii",
+        ascii_btn = wx.RadioButton(self, -1, "ASCII 1D", name="ascii",
             style=wx.RB_GROUP)
         ascii_btn.Bind(wx.EVT_RADIOBUTTON, self.datatype_changed)
         radio_sizer.Add(ascii_btn)
+        ascii2d_btn = wx.RadioButton(self, -1, "ASCII 2D", name="ascii2d")
+        ascii2d_btn.Bind(wx.EVT_RADIOBUTTON, self.datatype_changed)
+        radio_sizer.Add(ascii2d_btn)
         otoko_btn = wx.RadioButton(self, -1, "BSL 1D", name="otoko")
         otoko_btn.Bind(wx.EVT_RADIOBUTTON, self.datatype_changed)
         radio_sizer.Add(otoko_btn)
-        input_grid.Add(radio_sizer, (y,1), (1,1), wx.ALL, 5)
         bsl_btn = wx.RadioButton(self, -1, "BSL 2D", name="bsl")
         bsl_btn.Bind(wx.EVT_RADIOBUTTON, self.datatype_changed)
         radio_sizer.Add(bsl_btn)
+        input_grid.Add(radio_sizer, (y,1), (1,1), wx.ALL, 5)
         y += 1
 
@@ -549 +564 @@
         y += 1
 
-        iq_label = wx.StaticText(self, -1, "Intensity-Axis Data: ")
+        iq_label = wx.StaticText(self, -1, "Intensity Data: ")
         input_grid.Add(iq_label, (y,0), (1,1), wx.ALIGN_CENTER_VERTICAL, 5)
 
@@ -647 +662 @@
 
     def __init__(self, parent=None, title='File Converter', base=None,
-        manager=None, size=(PANEL_SIZE * 1.05, PANEL_SIZE / 1.1),
+        manager=None, size=(PANEL_SIZE * 0.96, PANEL_SIZE * 0.9),
         *args, **kwargs):
         kwargs['title'] = title

src/sas/sasgui/perspectives/file_converter/file_converter.py

@@ -25 +25 @@
         Returns a set of menu entries
         """
-        help_txt = "Convert single column ASCII data to CanSAS format"
+        help_txt = "Convert ASCII or BSL/OTOKO data to CanSAS or NXcanSAS formats"
         return [("File Converter", help_txt, self.on_file_converter)]
 

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

@@ -18 +18 @@
 *   Single-column ASCII data, with lines that end without any delimiter,
     or with a comma or semi-colon delimiter
+*   2D `ISIS ASCII formatted
+    <http://www.isis.stfc.ac.uk/instruments/loq/software/
+    colette-ascii-file-format-descriptions9808.pdf>`_ data
 *   `1D BSL/OTOKO format
     <http://www.diamond.ac.uk/Beamlines/Soft-Condensed-Matter/small-angle/
@@ -36 +39 @@
 
 1) Select the files containing your Q-axis and Intensity-axis data
-2) Choose whether the files are in ASCII, 1D BSL/OTOKO or 2D BSL/OTOKO format
+2) Choose whether the files are in ASCII 1D, ASCII 2D, 1D BSL/OTOKO or 2D BSL/OTOKO format
 3) Choose where you would like to save the converted file
 4) Optionally, input some metadata such as sample size, detector name, etc
@@ -47 +50 @@
 file, a dialog will appear asking which frames you would like converted. You
 may enter a start frame, end frame & increment, and all frames in that subset
-will be converted. For example, entering 0, 50 and 10 will convert frames 0, 
+will be converted. For example, entering 0, 50 and 10 will convert frames 0,
 10, 20, 30, 40 & 50.
 
@@ -56 +59 @@
 single file, so there is an option in the *Select Frame* dialog to output each
 frame to its own file. The single file option will produce one file with
-multiple `<SASdata>` elements. The multiple file option will output a separate 
-file with one `<SASdata>` element for each frame. The frame number will also be 
+multiple `<SASdata>` elements. The multiple file option will output a separate
+file with one `<SASdata>` element for each frame. The frame number will also be
 appended to the file name.
 
-The multiple file option is not available when exporting to NXcanSAS because 
+The multiple file option is not available when exporting to NXcanSAS because
 the HDF5 format is more efficient at handling large amounts of data.
 

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

@@ -257 +257 @@
         toks = os.path.splitext(label)
         path = os.path.join(models.find_plugins_dir(), toks[0])
+        message = "Are you sure you want to delete the file {}?".format(path)
+        dlg = wx.MessageDialog(self.frame, message, '', wx.YES_NO | wx.ICON_QUESTION)
+        if not dlg.ShowModal() == wx.ID_YES:
+            return
         try:
             for ext in ['.py', '.pyc']:
                 p_path = path + ext
+                if ext == '.pyc' and not os.path.isfile(path + ext):
+                    # If model is invalid, .pyc file may not exist as model has
+                    # never been compiled. Don't try and delete it
+                    continue
                 os.remove(p_path)
             self.update_custom_combo()
@@ -361 +369 @@
                                    'Add a new model function')
         wx.EVT_MENU(owner, wx_id, self.make_new_model)
-        
+
         wx_id = wx.NewId()
         self.edit_model_menu.Append(wx_id, 'Sum|Multi(p1, p2)',
@@ -383 +391 @@
           '(Re)Load all models present in user plugin_models folder')
         wx.EVT_MENU(owner, wx_id, self.load_plugin_models)
-                
+
     def set_edit_menu_helper(self, owner=None, menu=None):
         """
@@ -1734 +1742 @@
             @param unsmeared_error: data error, rescaled to unsmeared model
         """
-            
-        number_finite = np.count_nonzero(np.isfinite(y)) 
+
+        number_finite = np.count_nonzero(np.isfinite(y))
         np.nan_to_num(y)
         new_plot = self.create_theory_1D(x, y, page_id, model, data, state,
@@ -1794 +1802 @@
             msg = "Computing Error: Model did not return any finite value."
             wx.PostEvent(self.parent, StatusEvent(status = msg, info="error"))
-        else:                 
+        else:
             msg = "Computation  completed!"
             if number_finite != y.size:
@@ -1824 +1832 @@
         that can be plot.
         """
-        number_finite = np.count_nonzero(np.isfinite(image)) 
+        number_finite = np.count_nonzero(np.isfinite(image))
         np.nan_to_num(image)
         new_plot = Data2D(image=image, err_image=data.err_data)
@@ -1927 +1935 @@
                 ## and may be the cause of other noted instabilities
                 ##
-                ##    -PDB August 12, 2014 
+                ##    -PDB August 12, 2014
                 while self.calc_2D.isrunning():
                     time.sleep(0.1)
@@ -1969 +1977 @@
             if (self.calc_1D is not None) and self.calc_1D.isrunning():
                 self.calc_1D.stop()
-                ## stop just raises the flag -- the thread is supposed to 
+                ## stop just raises the flag -- the thread is supposed to
                 ## then kill itself but cannot.  Paul Kienzle came up with
                 ## this fix to prevent threads from stepping on each other
@@ -1981 +1989 @@
                 ## a request to stop the computation.
                 ## It seems thus that the whole thread approach used here
-                ## May need rethinking  
+                ## May need rethinking
                 ##
                 ##    -PDB August 12, 2014
@@ -2146 +2154 @@
             residuals.dxw = None
             residuals.ytransform = 'y'
-            # For latter scale changes 
+            # For latter scale changes
             residuals.xaxis('\\rm{Q} ', 'A^{-1}')
             residuals.yaxis('\\rm{Residuals} ', 'normalized')

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

@@ -186 +186 @@
             try:
                 model = load_custom_model(path)
-                model.name = PLUGIN_NAME_BASE + model.name
+                if not model.name.count(PLUGIN_NAME_BASE):
+                    model.name = PLUGIN_NAME_BASE + model.name
                 plugins[model.name] = model
             except Exception:
@@ -297 +298 @@
         for name, plug in self.stored_plugins.iteritems():
             self.model_dictionary[name] = plug
-        
+
         self._get_multifunc_models()
 

src/sas/sasgui/perspectives/pr/inversion_panel.py

@@ -70 +70 @@
         self.rg_ctl = None
         self.iq0_ctl = None
-        self.bck_chk = None
+        self.bck_value = None
+        self.bck_est_ctl = None
+        self.bck_man_ctl = None
+        self.est_bck = True
+        self.bck_input = None
         self.bck_ctl = None
 
@@ -312 +316 @@
         # Read the panel's parameters
         flag, alpha, dmax, nfunc, qmin, \
-        qmax, height, width = self._read_pars()
+        qmax, height, width, bck = self._read_pars()
 
         state.nfunc = nfunc
@@ -326 +330 @@
 
         # Background evaluation checkbox
-        state.estimate_bck = self.bck_chk.IsChecked()
+        state.estimate_bck = self.est_bck
+        state.bck_value = bck
 
         # Estimates
@@ -371 +376 @@
         self.plot_data.SetValue(str(state.file))
 
-        # Background evaluation checkbox
-        self.bck_chk.SetValue(state.estimate_bck)
+        # Background value
+        self.bck_est_ctl.SetValue(state.estimate_bck)
+        self.bck_man_ctl.SetValue(not state.estimate_bck)
+        if not state.estimate_bck:
+            self.bck_input.Enable()
+            self.bck_input.SetValue(str(state.bck_value))
+        self.est_bck = state.estimate_bck
+        self.bck_value = state.bck_value
 
         # Estimates
@@ -431 +442 @@
                        wx.EXPAND | wx.LEFT | wx.RIGHT | wx.ADJUST_MINSIZE, 15)
 
-        self.bck_chk = wx.CheckBox(self, -1, "Estimate background level")
-        hint_msg = "Check box to let the fit estimate "
-        hint_msg += "the constant background level."
-        self.bck_chk.SetToolTipString(hint_msg)
-        self.bck_chk.Bind(wx.EVT_CHECKBOX, self._on_pars_changed)
+        radio_sizer = wx.GridBagSizer(5, 5)
+
+        self.bck_est_ctl = wx.RadioButton(self, -1, "Estimate background level",
+            name="estimate_bck", style=wx.RB_GROUP)
+        self.bck_man_ctl = wx.RadioButton(self, -1, "Input manual background level",
+            name="manual_bck")
+
+        self.bck_est_ctl.Bind(wx.EVT_RADIOBUTTON, self._on_bck_changed)
+        self.bck_man_ctl.Bind(wx.EVT_RADIOBUTTON, self._on_bck_changed)
+
+        radio_sizer.Add(self.bck_est_ctl, (0,0), (1,1), wx.LEFT | wx.EXPAND)
+        radio_sizer.Add(self.bck_man_ctl, (0,1), (1,1), wx.RIGHT | wx.EXPAND)
+
         iy += 1
-        pars_sizer.Add(self.bck_chk, (iy, 0), (1, 2),
+        pars_sizer.Add(radio_sizer, (iy, 0), (1, 2),
                        wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
+
+        background_label = wx.StaticText(self, -1, "Background: ")
+        self.bck_input = PrTextCtrl(self, -1, style=wx.TE_PROCESS_ENTER,
+            size=(60, 20), value="0.0")
+        self.bck_input.Disable()
+        self.bck_input.Bind(wx.EVT_TEXT, self._read_pars)
+        background_units = wx.StaticText(self, -1, "[A^(-1)]", size=(55, 20))
+        iy += 1
+
+        background_sizer = wx.GridBagSizer(5, 5)
+
+        background_sizer.Add(background_label, (0, 0), (1,1),
+            wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 23)
+        background_sizer.Add(self.bck_input, (0, 1), (1,1),
+            wx.LEFT | wx.ADJUST_MINSIZE, 5)
+        background_sizer.Add(background_units, (0, 2), (1,1),
+            wx.LEFT | wx.ADJUST_MINSIZE, 5)
+        pars_sizer.Add(background_sizer, (iy, 0), (1, 2),
+            wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
+
         boxsizer1.Add(pars_sizer, 0, wx.EXPAND)
         vbox.Add(boxsizer1, (iy_vb, 0), (1, 1),
@@ -764 +803 @@
         self._on_pars_changed()
 
+    def _on_bck_changed(self, evt=None):
+        self.est_bck = self.bck_est_ctl.GetValue()
+        if self.est_bck:
+            self.bck_input.Disable()
+        else:
+            self.bck_input.Enable()
+
     def _on_pars_changed(self, evt=None):
         """
@@ -770 +816 @@
         scenes.
         """
-        flag, alpha, dmax, nfunc, qmin, qmax, height, width = self._read_pars()
-        has_bck = self.bck_chk.IsChecked()
+        flag, alpha, dmax, nfunc, qmin, qmax, height, width, bck = self._read_pars()
 
         # If the pars are valid, estimate alpha
@@ -783 +828 @@
                                                       d_max=dmax,
                                                       q_min=qmin, q_max=qmax,
-                                                      bck=has_bck,
+                                                      est_bck=self.est_bck,
+                                                      bck_val=bck,
                                                       height=height,
                                                       width=width)
@@ -797 +843 @@
         height = 0
         width = 0
+        background = 0
         flag = True
         # Read slit height
@@ -890 +937 @@
             self.qmax_ctl.Refresh()
 
-        return flag, alpha, dmax, nfunc, qmin, qmax, height, width
+        # Read background
+        if not self.est_bck:
+            try:
+                bck_str = self.bck_input.GetValue()
+                if len(bck_str.strip()) == 0:
+                    background = 0.0
+                else:
+                    background = float(bck_str)
+                    self.bck_input.SetBackgroundColour(wx.WHITE)
+            except ValueError:
+                background = 0.0
+                self.bck_input.SetBackgroundColour("pink")
+            self.bck_input.Refresh()
+
+        return flag, alpha, dmax, nfunc, qmin, qmax, height, width, background
 
     def _on_explore(self, evt):
@@ -915 +976 @@
         # Push it to the manager
 
-        flag, alpha, dmax, nfunc, qmin, qmax, height, width = self._read_pars()
-        has_bck = self.bck_chk.IsChecked()
+        flag, alpha, dmax, nfunc, qmin, qmax, height, width, bck = self._read_pars()
 
         if flag:
@@ -928 +988 @@
                                                    d_max=dmax,
                                                    q_min=qmin, q_max=qmax,
-                                                   bck=has_bck,
+                                                   est_bck=self.est_bck,
+                                                   bck_val = bck,
                                                    height=height,
                                                    width=width)

src/sas/sasgui/perspectives/pr/inversion_state.py

@@ -36 +36 @@
            ["qmin", "qmin"],
            ["qmax", "qmax"],
-           ["estimate_bck", "estimate_bck"]]
+           ["estimate_bck", "estimate_bck"],
+           ["bck_value", "bck_value"]]
 
 ## List of P(r) inversion outputs
@@ -62 +63 @@
         self.estimate_bck = False
         self.timestamp = time.time()
+        self.bck_value = 0.0
 
         # Inversion parameters
@@ -109 +111 @@
         state += "Timestamp:    %s\n" % self.timestamp
         state += "Estimate bck: %s\n" % str(self.estimate_bck)
+        state += "Bck Value:    %s\n" % str(self.bck_value)
         state += "No. terms:    %s\n" % str(self.nfunc)
         state += "D_max:        %s\n" % str(self.d_max)
@@ -296 +299 @@
                             self.coefficients.append(float(c))
                         except:
-                            # Bad data, skip. We will count the number of 
-                            # coefficients at the very end and deal with 
+                            # Bad data, skip. We will count the number of
+                            # coefficients at the very end and deal with
                             # inconsistencies then.
                             pass
@@ -329 +332 @@
                                 cov_row.append(float(c))
                             except:
-                                # Bad data, skip. We will count the number of 
-                                # coefficients at the very end and deal with 
+                                # Bad data, skip. We will count the number of
+                                # coefficients at the very end and deal with
                                 # inconsistencies then.
                                 pass
@@ -461 +464 @@
                 tree = etree.parse(path, parser=etree.ETCompatXMLParser())
                 # Check the format version number
-                # Specifying the namespace will take care of the file 
-                #format version 
+                # Specifying the namespace will take care of the file
+                #format version
                 root = tree.getroot()
 

src/sas/sasgui/perspectives/pr/media/pr_help.rst

@@ -49 +49 @@
 P(r) inversion requires that the background be perfectly subtracted.  This is
 often difficult to do well and thus many data sets will include a background.
-For those cases, the user should check the "estimate background" box and the
-module will do its best to estimate it.
+For those cases, the user should check the "Estimate background level" option
+and the module will do its best to estimate it. If you know the background value
+for your data, select the "Input manual background level" option. Note that
+this value will be treated as having 0 error.
 
 The P(r) module is constantly computing in the background what the optimum

src/sas/sasgui/perspectives/pr/pr.py

@@ -68 +68 @@
         self.q_min = None
         self.q_max = None
-        self.has_bck = False
+        self.est_bck = False
+        self.bck_val = 0
         self.slit_height = 0
         self.slit_width = 0
@@ -828 +829 @@
         self.control_panel.iq0 = pr.iq0(out)
         self.control_panel.bck = pr.background
+        self.control_panel.bck_input.SetValue("{:.2g}".format(pr.background))
 
         # Show I(q) fit
@@ -907 +909 @@
 
     def setup_plot_inversion(self, alpha, nfunc, d_max, q_min=None, q_max=None,
-                             bck=False, height=0, width=0):
+                             est_bck=False, bck_val=0, height=0, width=0):
         """
             Set up inversion from plotted data
@@ -916 +918 @@
         self.q_min = q_min
         self.q_max = q_max
-        self.has_bck = bck
+        self.est_bck = est_bck
+        self.bck_val = bck_val
         self.slit_height = height
         self.slit_width = width
@@ -930 +933 @@
     def estimate_plot_inversion(self, alpha, nfunc, d_max,
                                 q_min=None, q_max=None,
-                                bck=False, height=0, width=0):
+                                est_bck=False, bck_val=0, height=0, width=0):
         """
             Estimate parameters from plotted data
@@ -939 +942 @@
         self.q_min = q_min
         self.q_max = q_max
-        self.has_bck = bck
+        self.est_bck = est_bck
+        self.bck_val = bck_val
         self.slit_height = height
         self.slit_width = width
@@ -973 +977 @@
         pr.x = self.current_plottable.x
         pr.y = self.current_plottable.y
-        pr.has_bck = self.has_bck
+        pr.est_bck = self.est_bck
         pr.slit_height = self.slit_height
         pr.slit_width = self.slit_width
+        pr.background = self.bck_val
 
         # Keep track of the plot window title to ensure that
@@ -1019 +1024 @@
         self.q_min = q_min
         self.q_max = q_max
-        self.has_bck = bck
+        self.est_bck = bck
         self.slit_height = height
         self.slit_width = width
@@ -1042 +1047 @@
         self.q_min = q_min
         self.q_max = q_max
-        self.has_bck = bck
+        self.est_bck = bck
         self.slit_height = height
         self.slit_width = width
@@ -1115 +1120 @@
             pr.y = y
             pr.err = err
-            pr.has_bck = self.has_bck
+            pr.est_bck = self.est_bck
             pr.slit_height = self.slit_height
             pr.slit_width = self.slit_width

src/sas/sasgui/perspectives/corfunc/corfunc.py

@@ -189 +189 @@
             # Show the transformation as a curve instead of points
             new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
+        elif label == IDF_LABEL:
+            new_plot.xaxis("{x}", 'A')
+            new_plot.yaxis("{g_1}", '')
+            # Linear scale
+            new_plot.xtransform = 'x'
+            new_plot.ytransform = 'y'
+            group_id = GROUP_ID_IDF
+            # Show IDF as a curve instead of points
+            new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
         new_plot.id = label
         new_plot.name = label

src/sas/sasgui/perspectives/corfunc/corfunc_panel.py

@@ -55 +55 @@
         self._data = data # The data to be analysed (corrected fr background)
         self._extrapolated_data = None # The extrapolated data set
+        # Callable object of class CorfuncCalculator._Interpolator representing
+        # the extrapolated and interpolated data
+        self._extrapolated_fn = None
         self._transformed_data = None # Fourier trans. of the extrapolated data
         self._calculator = CorfuncCalculator()
@@ -218 +221 @@
 
         try:
-            params, self._extrapolated_data = self._calculator.compute_extrapolation()
+            params, self._extrapolated_data, self._extrapolated_fn = \
+                self._calculator.compute_extrapolation()
         except Exception as e:
             msg = "Error extrapolating data:\n"
@@ -257 +261 @@
             StatusEvent(status=msg))
 
-    def transform_complete(self, transform=None):
+    def transform_complete(self, transforms=None):
         """
         Called from FourierThread when calculation has completed
         """
         self._transform_btn.SetLabel("Transform")
-        if transform is None:
+        if transforms is None:
             msg = "Error calculating Transform."
             if self.transform_type == 'hilbert':
@@ -270 +274 @@
             self._extract_btn.Disable()
             return
-        self._transformed_data = transform
-        import numpy as np
-        plot_x = transform.x[np.where(transform.x <= 200)]
-        plot_y = transform.y[np.where(transform.x <= 200)]
+
+        self._transformed_data = transforms
+        (transform1, transform3, idf) = transforms
+        plot_x = transform1.x[transform1.x <= 200]
+        plot_y = transform1.y[transform1.x <= 200]
         self._manager.show_data(Data1D(plot_x, plot_y), TRANSFORM_LABEL1)
+        # No need to shorten gamma3 as it's only calculated up to x=200
+        self._manager.show_data(transform3, TRANSFORM_LABEL3)
+
+        plot_x = idf.x[idf.x <= 200]
+        plot_y = idf.y[idf.x <= 200]
+        self._manager.show_data(Data1D(plot_x, plot_y), IDF_LABEL)
+
         # Only enable extract params button if a fourier trans. has been done
         if self.transform_type == 'fourier':
@@ -286 +298 @@
         """
         try:
-            params = self._calculator.extract_parameters(self._transformed_data)
+            params = self._calculator.extract_parameters(self._transformed_data[0])
         except:
             params = None

src/sas/sasgui/perspectives/corfunc/corfunc_state.py

@@ -59 +59 @@
         self.q = None
         self.iq = None
-        # TODO: Add extrapolated data and transformed data (when implemented)
 
     def __str__(self):

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

@@ -10 +10 @@
 
 This performs a correlation function analysis of one-dimensional
-SAXS/SANS data, or generates a model-independent volume fraction 
+SAXS/SANS data, or generates a model-independent volume fraction
 profile from the SANS from an adsorbed polymer/surfactant layer.
 
-A correlation function may be interpreted in terms of an imaginary rod moving 
-through the structure of the material. Γ\ :sub:`1D`\ (R) is the probability that 
-a rod of length R moving through the material has equal electron/neutron scattering 
-length density at either end. Hence a frequently occurring spacing within a structure 
+A correlation function may be interpreted in terms of an imaginary rod moving
+through the structure of the material. Γ\ :sub:`1D`\ (R) is the probability that
+a rod of length R moving through the material has equal electron/neutron scattering
+length density at either end. Hence a frequently occurring spacing within a structure
 manifests itself as a peak.
 
@@ -30 +30 @@
 *  Fourier / Hilbert Transform of the smoothed data to give the correlation
    function / volume fraction profile, respectively
-*  (Optional) Interpretation of the 1D correlation function based on an ideal 
+*  (Optional) Interpretation of the 1D correlation function based on an ideal
    lamellar morphology
 
@@ -74 +74 @@
    :align: center
 
-   
+
 Smoothing
 ---------
 
-The extrapolated data set consists of the Guinier back-extrapolation from Q~0 
+The extrapolated data set consists of the Guinier back-extrapolation from Q~0
 up 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.
 
@@ -93 +93 @@
     h_i = \frac{1}{1 + \frac{(x_i-b)^2}{(x_i-a)^2}}
 
-        
+
 Transform
 ---------
@@ -102 +102 @@
 If "Fourier" is selected for the transform type, the analysis will perform a
 discrete cosine transform on the extrapolated data in order to calculate the
-correlation function
+1D correlation function:
 
 .. math::
@@ -115 +115 @@
     \left(n + \frac{1}{2} \right) k \right] } \text{ for } k = 0, 1, \ldots,
     N-1, N
+
+The 3D correlation function is also calculated:
+
+.. math::
+    \Gamma _{3D}(R) = \frac{1}{Q^{*}} \int_{0}^{\infty}I(q) q^{2}
+    \frac{sin(qR)}{qR} dq
 
 Hilbert
@@ -165 +171 @@
 .. figure:: profile1.png
    :align: center
- 
+
 .. figure:: profile2.png
    :align: center
-   
+
 
 References
@@ -191 +197 @@
 -----
 Upon sending data for correlation function analysis, it will be plotted (minus
-the background value), along with a *red* bar indicating the *upper end of the 
+the background value), along with a *red* bar indicating the *upper end of the
 low-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
 dragging, or by entering appropriate values in the Q range input boxes.
@@ -221 +227 @@
     :align: center
 
-        
+
 .. note::
     This help document was last changed by Steve King, 08Oct2016

src/sas/sasgui/perspectives/corfunc/plot_labels.py

@@ -4 +4 @@
 
 GROUP_ID_TRANSFORM = r"$\Gamma(x)$"
-TRANSFORM_LABEL1 = r"$\Gamma1(x)$"
-TRANSFORM_LABEL3 = r"$\Gamma3(x)$"
+TRANSFORM_LABEL1 = r"$\Gamma_1(x)$"
+TRANSFORM_LABEL3 = r"$\Gamma_3(x)$"
+
+GROUP_ID_IDF = r"$g_1(x)$"
+IDF_LABEL = r"$g_1(x)$"