Changeset 69363c7 in sasview for src/sas/sascalc/pr

Timestamp:

Sep 22, 2017 10:29:48 AM (7 years ago)

Author:

Paul Kienzle <pkienzle@…>

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:

ab0b93f

Parents:

1386b2f (diff), d76c43a (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@…> (09/22/17 10:28:48)

git-committer:

Paul Kienzle <pkienzle@…> (09/22/17 10:29:48)

Message:

Merge branch 'master' into ticket-853-fit-gui-to-calc

Location:

src/sas/sascalc/pr

Files:

• c_extensions/Cinvertor.c (modified) (7 diffs)
• c_extensions/invertor.c (modified) (2 diffs)
• c_extensions/invertor.h (modified) (1 diff)
• invertor.py (modified) (10 diffs)
• fit/AbstractFitEngine.py (modified) (24 diffs)

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/sascalc/pr/fit/AbstractFitEngine.py

@@ -137 +137 @@
                that will smear the theory data (slit smearing or resolution
                smearing) when set.
-            
+
             The proper way to set the smearing object would be to
             do the following: ::
-            
-                from sas.sascalc.data_util.qsmearing import smear_selection
+
+                from sas.sascalc.fit.qsmearing import smear_selection
                 smearer = smear_selection(some_data)
                 fitdata1d = FitData1D( x= [1,3,..,],
@@ -147 +147 @@
                                         dx=None,
                                         dy=[1,2...], smearer= smearer)
-           
+
             :Note: that some_data _HAS_ to be of
                 class DataLoader.data_info.Data1D
                 Setting it back to None will turn smearing off.
-                
+
         """
         Data1D.__init__(self, x=x, y=y, dx=dx, dy=dy)
@@ -176 +176 @@
         ## Max Q-value
         self.qmax = max(self.x)
-        
+
         # Range used for input to smearing
         self._qmin_unsmeared = self.qmin
@@ -184 +184 @@
         self.idx_unsmeared = (self.x >= self._qmin_unsmeared) \
                             & (self.x <= self._qmax_unsmeared)
-  
+
     def set_fit_range(self, qmin=None, qmax=None):
         """ to set the fit range"""
@@ -199 +199 @@
         self._qmin_unsmeared = self.qmin
         self._qmax_unsmeared = self.qmax
-        
+
         self._first_unsmeared_bin = 0
         self._last_unsmeared_bin = len(self.x) - 1
-        
+
         if self.smearer is not None:
             self._first_unsmeared_bin, self._last_unsmeared_bin = \
@@ -208 +208 @@
             self._qmin_unsmeared = self.x[self._first_unsmeared_bin]
             self._qmax_unsmeared = self.x[self._last_unsmeared_bin]
-            
+
         # Identify the bin range for the unsmeared and smeared spaces
         self.idx = (self.x >= self.qmin) & (self.x <= self.qmax)
@@ -231 +231 @@
         """
             Compute residuals.
-            
+
             If self.smearer has been set, use if to smear
             the data before computing chi squared.
-            
+
             :param fn: function that return model value
-            
+
             :return: residuals
         """
@@ -242 +242 @@
         fx = np.zeros(len(self.x))
         fx[self.idx_unsmeared] = fn(self.x[self.idx_unsmeared])
-       
+
         ## Smear theory data
         if self.smearer is not None:
@@ -253 +253 @@
             raise RuntimeError, msg
         return (self.y[self.idx] - fx[self.idx]) / self.dy[self.idx], fx[self.idx]
-            
+
     def residuals_deriv(self, model, pars=[]):
         """
             :return: residuals derivatives .
-            
-            :note: in this case just return empty array 
+
+            :note: in this case just return empty array
         """
         return []
@@ -293 +293 @@
         x_max = max(math.fabs(sas_data2d.xmin), math.fabs(sas_data2d.xmax))
         y_max = max(math.fabs(sas_data2d.ymin), math.fabs(sas_data2d.ymax))
-        
+
         ## fitting range
         if qmin is None:
@@ -305 +305 @@
             self.res_err_data = copy.deepcopy(self.err_data)
         #self.res_err_data[self.res_err_data==0]=1
-        
+
         self.radius = np.sqrt(self.qx_data**2 + self.qy_data**2)
-        
+
         # Note: mask = True: for MASK while mask = False for NOT to mask
         self.idx = ((self.qmin <= self.radius) &\
@@ -371 +371 @@
 
         return res, gn
-        
+
     def residuals_deriv(self, model, pars=[]):
         """
         :return: residuals derivatives .
-        
+
         :note: in this case just return empty array
-        
+
         """
         return []
-    
-    
+
+
 class FitAbort(Exception):
     """
@@ -399 +399 @@
         self.fit_arrange_dict = {}
         self.fitter_id = None
-        
+
     def set_model(self, model, id, pars=[], constraints=[], data=None):
         """
         set a model on a given  in the fit engine.
-        
-        :param model: sas.models type 
+
+        :param model: sas.models type
         :param id: is the key of the fitArrange dictionary where model is saved as a value
-        :param pars: the list of parameters to fit 
-        :param constraints: list of 
+        :param pars: the list of parameters to fit
+        :param constraints: list of
             tuple (name of parameter, value of parameters)
             the value of parameter must be a string to constraint 2 different
             parameters.
-            Example:  
+            Example:
             we want to fit 2 model M1 and M2 both have parameters A and B.
             constraints can be ``constraints = [(M1.A, M2.B+2), (M1.B= M2.A *5),...,]``
-            
-             
+
+
         :note: pars must contains only name of existing model's parameters
-        
+
         """
         if not pars:
@@ -448 +448 @@
         in a FitArrange object and adds that object in a dictionary
         with key id.
-        
+
         :param data: data added
         :param id: unique key corresponding to a fitArrange object with data
@@ -459 +459 @@
                                  dx=data.dx, dy=data.dy, smearer=smearer)
         fitdata.sas_data = data
-       
+
         fitdata.set_fit_range(qmin=qmin, qmax=qmax)
         #A fitArrange is already created but contains model only at id
@@ -469 +469 @@
             fitproblem.add_data(fitdata)
             self.fit_arrange_dict[id] = fitproblem
-   
+
     def get_model(self, id):
         """
         :param id: id is key in the dictionary containing the model to return
-        
+
         :return:  a model at this id or None if no FitArrange element was
             created with this id
@@ -481 +481 @@
         else:
             return None
-    
+
     def remove_fit_problem(self, id):
         """remove   fitarrange in id"""
         if id in self.fit_arrange_dict:
             del self.fit_arrange_dict[id]
-            
+
     def select_problem_for_fit(self, id, value):
         """
         select a couple of model and data at the id position in dictionary
         and set in self.selected value to value
-        
+
         :param value: the value to allow fitting.
                 can only have the value one or zero
@@ -497 +497 @@
         if id in self.fit_arrange_dict:
             self.fit_arrange_dict[id].set_to_fit(value)
-             
+
     def get_problem_to_fit(self, id):
         """
         return the self.selected value of the fit problem of id
-        
+
         :param id: the id of the problem
         """
         if id in self.fit_arrange_dict:
             self.fit_arrange_dict[id].get_to_fit()
-    
-    
+
+
 class FitArrange:
     def __init__(self):
@@ -514 +514 @@
         to perform the Fit.FitArrange must contain exactly one model
         and at least one data for the fit to be performed.
-        
+
         model: the model selected by the user
         Ldata: a list of data what the user wants to fit
-            
+
         """
         self.model = None
@@ -528 +528 @@
         """
         set_model save a copy of the model
-        
+
         :param model: the model being set
         """
         self.model = model
-        
+
     def add_data(self, data):
         """
         add_data fill a self.data_list with data to fit
-        
+
         :param data: Data to add in the list
         """
         if not data in self.data_list:
             self.data_list.append(data)
-            
+
     def get_model(self):
         """
@@ -547 +547 @@
         """
         return self.model
-     
+
     def get_data(self):
         """
@@ -553 +553 @@
         """
         return self.data_list[0]
-      
+
     def remove_data(self, data):
         """
         Remove one element from the list
-        
+
         :param data: Data to remove from data_list
         """
         if data in self.data_list:
             self.data_list.remove(data)
-            
+
     def set_to_fit(self, value=0):
         """
         set self.selected to 0 or 1  for other values raise an exception
-        
+
         :param value: integer between 0 or 1
         """
         self.selected = value
-        
+
     def get_to_fit(self):
         """
@@ -602 +602 @@
         if self.model is not None and self.data is not None:
             self.inputs = [(self.model, self.data)]
-     
+
     def set_model(self, model):
         """
         """
         self.model = model
-        
+
     def set_fitness(self, fitness):
         """
         """
         self.fitness = fitness
-        
+
     def __str__(self):
         """
@@ -627 +627 @@
         msg = [msg1, msg3] + msg2
         return "\n".join(msg)
-    
+
     def print_summary(self):
         """