Changeset a06ee7e in sasview

Timestamp:

Aug 17, 2017 7:42:30 AM (7 years ago)

Author:

GitHub <noreply@…>

Branches:

master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload

Children:

fca1f50, 0b6f83c, 7b15990, f001bc9

Parents:

fcfaf52 (diff), 07ec714 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Paul Kienzle <pkienzle@…> (08/17/17 07:42:30)

git-committer:

GitHub <noreply@…> (08/17/17 07:42:30)

Message:

Merge pull request #96 from lewisodriscoll/ticket-864

Bug Fixes and Improvements

Files:

• src/sas/sascalc/pr/c_extensions/Cinvertor.c (modified) (7 diffs)
• src/sas/sascalc/pr/c_extensions/invertor.c (modified) (2 diffs)
• src/sas/sascalc/pr/c_extensions/invertor.h (modified) (1 diff)
• src/sas/sascalc/pr/invertor.py (modified) (10 diffs)
• src/sas/sasgui/perspectives/calculator/model_editor.py (modified) (16 diffs)
• src/sas/sasgui/perspectives/calculator/pyconsole.py (modified) (2 diffs)
• src/sas/sasgui/perspectives/fitting/fitting.py (modified) (10 diffs)
• src/sas/sasgui/perspectives/fitting/models.py (modified) (2 diffs)
• src/sas/sasgui/perspectives/pr/inversion_panel.py (modified) (12 diffs)
• src/sas/sasgui/perspectives/pr/inversion_state.py (modified) (6 diffs)
• src/sas/sasgui/perspectives/pr/media/pr_help.rst (modified) (1 diff)
• src/sas/sasgui/perspectives/pr/pr.py (modified) (10 diffs)
• test/pr_inversion/test/utest_invertor.py (modified) (1 diff)
• docs/sphinx-docs/build_sphinx.py (modified) (1 diff)

src/sas/sascalc/pr/c_extensions/Cinvertor.c

@@ -294 +294 @@
 }
 
-const char set_has_bck_doc[] =
+const char set_est_bck_doc[] =
         "Sets background flag\n";
 
@@ -300 +300 @@
  * Sets the maximum distance
  */
-static PyObject * set_has_bck(Cinvertor *self, PyObject *args) {
-        int has_bck;
-
-        if (!PyArg_ParseTuple(args, "i", &has_bck)) return NULL;
-        self->params.has_bck = has_bck;
-        return Py_BuildValue("i", self->params.has_bck);
-}
-
-const char get_has_bck_doc[] =
+static PyObject * set_est_bck(Cinvertor *self, PyObject *args) {
+        int est_bck;
+
+        if (!PyArg_ParseTuple(args, "i", &est_bck)) return NULL;
+        self->params.est_bck = est_bck;
+        return Py_BuildValue("i", self->params.est_bck);
+}
+
+const char get_est_bck_doc[] =
         "Gets background flag\n";
 
@@ -314 +314 @@
  * Gets the maximum distance
  */
-static PyObject * get_has_bck(Cinvertor *self, PyObject *args) {
-        return Py_BuildValue("i", self->params.has_bck);
+static PyObject * get_est_bck(Cinvertor *self, PyObject *args) {
+        return Py_BuildValue("i", self->params.est_bck);
 }
 
@@ -882 +882 @@
         sqrt_alpha = sqrt(self->params.alpha);
         pi = acos(-1.0);
-        offset = (self->params.has_bck==1) ? 0 : 1;
+        offset = (self->params.est_bck==1) ? 0 : 1;
 
     for (j=0; j<nfunc; j++) {
@@ -892 +892 @@
             }
             if (accept_q(self, self->params.x[i])){
-                if (self->params.has_bck==1 && j==0) {
+                if (self->params.est_bck==1 && j==0) {
                     a[i*nfunc+j] = 1.0/self->params.err[i];
                 } else {
@@ -906 +906 @@
         }
         for (i_r=0; i_r<nr; i_r++){
-            if (self->params.has_bck==1 && j==0) {
+            if (self->params.est_bck==1 && j==0) {
                 a[(i_r+self->params.npoints)*nfunc+j] = 0.0;
             } else {
@@ -1029 +1029 @@
                    {"set_slit_height", (PyCFunction)set_slit_height, METH_VARARGS, set_slit_height_doc},
                    {"get_slit_height", (PyCFunction)get_slit_height, METH_VARARGS, get_slit_height_doc},
-                   {"set_has_bck", (PyCFunction)set_has_bck, METH_VARARGS, set_has_bck_doc},
-                   {"get_has_bck", (PyCFunction)get_has_bck, METH_VARARGS, get_has_bck_doc},
+                   {"set_est_bck", (PyCFunction)set_est_bck, METH_VARARGS, set_est_bck_doc},
+                   {"get_est_bck", (PyCFunction)get_est_bck, METH_VARARGS, get_est_bck_doc},
                    {"get_nx", (PyCFunction)get_nx, METH_VARARGS, get_nx_doc},
                    {"get_ny", (PyCFunction)get_ny, METH_VARARGS, get_ny_doc},

src/sas/sascalc/pr/c_extensions/invertor.c

@@ -20 +20 @@
         pars->q_min = -1.0;
         pars->q_max = -1.0;
-        pars->has_bck = 0;
+        pars->est_bck = 0;
 }
 
@@ -313 +313 @@
     return sqrt(sum_r2/(2.0*sum));
 }
-

src/sas/sascalc/pr/c_extensions/invertor.h

@@ -27 +27 @@
     double q_max;
     /// Flag for whether or not to evalute a constant background while inverting
-    int has_bck;
+    int est_bck;
     /// Slit height in units of q [A-1]
     double slit_height;

src/sas/sascalc/pr/invertor.py

@@ -121 +121 @@
          self.q_min, self.q_max,
          self.x, self.y,
-         self.err, self.has_bck,
+         self.err, self.est_bck,
          self.slit_height, self.slit_width) = state
 
@@ -133 +133 @@
                  self.q_min, self.q_max,
                  self.x, self.y,
-                 self.err, self.has_bck,
+                 self.err, self.est_bck,
                  self.slit_height, self.slit_width,
                 )
@@ -175 +175 @@
         elif name == 'slit_width':
             return self.set_slit_width(value)
-        elif name == 'has_bck':
+        elif name == 'est_bck':
             if value == True:
-                return self.set_has_bck(1)
+                return self.set_est_bck(1)
             elif value == False:
-                return self.set_has_bck(0)
+                return self.set_est_bck(0)
             else:
-                raise ValueError, "Invertor: has_bck can only be True or False"
+                raise ValueError, "Invertor: est_bck can only be True or False"
 
         return Cinvertor.__setattr__(self, name, value)
@@ -220 +220 @@
         elif name == 'slit_width':
             return self.get_slit_width()
-        elif name == 'has_bck':
-            value = self.get_has_bck()
+        elif name == 'est_bck':
+            value = self.get_est_bck()
             if value == 1:
                 return True
@@ -248 +248 @@
         invertor.y = self.y
         invertor.err = self.err
-        invertor.has_bck = self.has_bck
+        invertor.est_bck = self.est_bck
+        invertor.background = self.background
         invertor.slit_height = self.slit_height
         invertor.slit_width = self.slit_width
@@ -290 +291 @@
         """
         # Reset the background value before proceeding
-        self.background = 0.0
-        return self.lstsq(nfunc, nr=nr)
+        # self.background = 0.0
+        if not self.est_bck:
+            self.y -= self.background
+        out, cov = self.lstsq(nfunc, nr=nr)
+        if not self.est_bck:
+            self.y += self.background
+        return out, cov
 
     def iq(self, out, q):
@@ -454 +460 @@
 
         # If we need to fit the background, add a term
-        if self.has_bck == True:
+        if self.est_bck == True:
             nfunc_0 = nfunc
             nfunc += 1
@@ -500 +506 @@
 
         # Keep a copy of the last output
-        if self.has_bck == False:
-            self.background = 0
+        if self.est_bck == False:
             self.out = c
             self.cov = err
@@ -653 +658 @@
         file.write("#slit_width=%g\n" % self.slit_width)
         file.write("#background=%g\n" % self.background)
-        if self.has_bck == True:
+        if self.est_bck == True:
             file.write("#has_bck=1\n")
         else:
@@ -734 +739 @@
                         toks = line.split('=')
                         if int(toks[1]) == 1:
-                            self.has_bck = True
+                            self.est_bck = True
                         else:
-                            self.has_bck = False
+                            self.est_bck = False
 
                     # Now read in the parameters

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/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

test/pr_inversion/test/utest_invertor.py

@@ -68 +68 @@
             self.x_in[i] = 1.0*(i+1)
 
-    def test_has_bck_flag(self):
-        """
-            Tests the has_bck flag operations
-        """
-        self.assertEqual(self.invertor.has_bck, False)
-        self.invertor.has_bck=True
-        self.assertEqual(self.invertor.has_bck, True)
+    def test_est_bck_flag(self):
+        """
+            Tests the est_bck flag operations
+        """
+        self.assertEqual(self.invertor.est_bck, False)
+        self.invertor.est_bck=True
+        self.assertEqual(self.invertor.est_bck, True)
         def doit_float():
-            self.invertor.has_bck  = 2.0
+            self.invertor.est_bck  = 2.0
         def doit_str():
-            self.invertor.has_bck  = 'a'
+            self.invertor.est_bck  = 'a'
 
         self.assertRaises(ValueError, doit_float)

docs/sphinx-docs/build_sphinx.py

@@ -38 +38 @@
 #/sasview-local-trunk/docs/sphinx-docs/build_sphinx.py
 SASMODELS_SOURCE_PROLOG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc")
-SASMODELS_SOURCE_GPU = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "ref", "gpu")
-SASMODELS_SOURCE_SESANS = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "ref", "sesans")
-SASMODELS_SOURCE_SESANSIMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "ref", "sesans", "sesans_img")
-SASMODELS_SOURCE_MAGNETISM = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "ref", "magnetism")
-SASMODELS_SOURCE_MAGIMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "ref", "magnetism", "mag_img")
-SASMODELS_SOURCE_REF_MODELS = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "ref", "models")
+SASMODELS_SOURCE_GPU = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "gpu")
+SASMODELS_SOURCE_SESANS = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "sesans")
+SASMODELS_SOURCE_SESANSIMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "sesans", "sesans_img")
+SASMODELS_SOURCE_MAGNETISM = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "magnetism")
+SASMODELS_SOURCE_MAGIMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "magnetism", "mag_img")
+SASMODELS_SOURCE_REF_MODELS = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "guide", "models")
 SASMODELS_SOURCE_MODELS = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "model")
 SASMODELS_SOURCE_IMG = os.path.join(CURRENT_SCRIPT_DIR, "..", "..", "..", "sasmodels", "doc", "model", "img")