Bug 3020: The values of a fitting points are filled correctly.

Author: shoops

copasi/parameterFitting/CExperiment.cpp

@@ -354,7 +354,7 @@ void CExperiment::updateFittedPoints()
       }
 }
 
-void CExperiment::updateFittedPointValues(const size_t & index, bool includeSimulation)
+void CExperiment::updateFittedPointValues(const size_t & index)
 {
   CDataVector< CFittingPoint >::iterator it = mFittingPoints.begin();
   CDataVector< CFittingPoint >::iterator end = mFittingPoints.end();
@@ -395,7 +395,7 @@ void CExperiment::updateFittedPointValues(const size_t & index, bool includeSimu
 
       it->setValues(Independent,
                     *pDataDependent,
-                    includeSimulation ? *pDataDependentCalculated : std::numeric_limits<C_FLOAT64>::quiet_NaN(),
+                    *pDataDependentCalculated,
                     Residual);
     }
 

copasi/parameterFitting/CExperiment.h

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2021 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -358,13 +358,10 @@ class CExperiment: public CCopasiParameterGroup
 
   /**
    * This method is used for output to fill the fitted points
-   * with the values of the index data record. If index exceedds the
+   * with the values of the index data record. If index exceeds the
    * number of data records all values are set to NaN.
-   * If includeSimulation = false the entries for the simulation results
-   * are set to NaN. (This means the simulated time series is not plotted and
-   * can be output using a different mechanism)
    */
-  void updateFittedPointValues(const size_t & index, bool includeSimulation);
+  void updateFittedPointValues(const size_t & index);
 
   /**
    * Fill the fitted points with values from the extended time series

copasi/parameterFitting/CExperimentSet.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2021 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -288,35 +288,40 @@ bool CExperimentSet::calculateStatistics()
     }
 
   // This is the time to call the output handler to plot the fitted points.
-  for (it = mpExperiments->begin() + mNonExperiments, imax = 0; it != end; ++it)
-    imax = std::max(imax, (*it)->getDependentData().numRows());
+  size_t j, jmax;
+
+  imax = 0;
+
+  for (it = mpExperiments->begin() + mNonExperiments; it != end; ++it)
+    {
+      imax = std::max(imax, (*it)->getDependentData().numRows());
+    }
 
   CCopasiTask * pParentTask = dynamic_cast< CCopasiTask *>(getObjectAncestor("Task"));
   assert(pParentTask != NULL);
 
-  for (i = 0; i < imax; i++)
+  for (i = 0, j = 0; i < imax; i++)
     {
       for (it = mpExperiments->begin() + mNonExperiments; it != end; ++it)
-        (*it)->updateFittedPointValues(i, (*it)->getExperimentType() != CTaskEnum::Task::timeCourse); //false means without simulated data
+        (*it)->updateFittedPointValues(i);
 
       pParentTask->output(COutputInterface::AFTER);
-    }
 
-  //now the extended time series
-  for (it = mpExperiments->begin() + mNonExperiments, imax = 0; it != end; ++it)
-    imax = std::max(imax, (*it)->extendedTimeSeriesSize());
+      // TODO the 3 below relies on the fact that currently the number of intermittend point is CFitProblem::numIntermediateSteps
+      jmax = std::min(j + 3, (imax - 1) * 3);
 
-  for (i = 0; i < imax; i++)
-    {
-      for (it = mpExperiments->begin() + mNonExperiments; it != end; ++it)
+      for (; j < jmax; j++)
         {
-          if ((*it)->getExperimentType() == CTaskEnum::Task::timeCourse)
+          for (it = mpExperiments->begin() + mNonExperiments; it != end; ++it)
             {
-              (*it)->updateFittedPointValuesFromExtendedTimeSeries(i);
+              if ((*it)->getExperimentType() == CTaskEnum::Task::timeCourse)
+                {
+                  (*it)->updateFittedPointValuesFromExtendedTimeSeries(j);
+                }
             }
-        }
 
-      pParentTask->output(COutputInterface::AFTER);
+          pParentTask->output(COutputInterface::AFTER);
+        }
     }
 
   return true;
@@ -340,7 +345,6 @@ const CVector< C_FLOAT64 > & CExperimentSet::getDependentErrorMeanSD() const
 const CVector< size_t > & CExperimentSet::getDependentDataCount() const
 {return mDependentDataCount;}
 
-
 size_t CExperimentSet::getExperimentCount() const
 {return size() - mNonExperiments;}
 

copasi/parameterFitting/CFitProblem.cpp

@@ -560,7 +560,7 @@ bool CFitProblem::initialize()
     }
 
   mCompleteInitialState = mpContainer->getCompleteInitialState();
-  mpInitialStateTime = mpContainer->getInitialState().array() + mpContainer->getCountFixedEventTargets();
+  mpInitialStateTime = mpContainer->getInitialState().array() + mpContainer->getCountFixed() + mpContainer->getCountFixedEventTargets();
 
   success &= mpExperimentSet->compile(mpContainer);
 
@@ -943,7 +943,7 @@ bool CFitProblem::calculate()
 
   size_t i, imax = mpExperimentSet->getExperimentCount();
   size_t j;
-  size_t kmax;
+  int kmax;
   mCalculateValue = 0.0;
 
   CExperiment * pExp = NULL;
@@ -1063,7 +1063,7 @@ bool CFitProblem::calculate()
                     //calculate a reasonable number of intermediate points
                     numIntermediateSteps = 4; //TODO
                     //resize the storage for the extended time series
-                    pExp->initExtendedTimeSeries(numIntermediateSteps * (kmax > 0 ? kmax - 1 : 0) + 1);
+                    pExp->initExtendedTimeSeries(numIntermediateSteps * std::max(kmax - 1, 0));
                   }
 
                 for (j = 0; j < kmax && Continue; j++) // For each data row;
@@ -1145,8 +1145,6 @@ bool CFitProblem::calculate()
                     if (mStoreResults)
                       {
                         mCalculateValue += pExp->sumOfSquaresStore(j, DependentValues);
-                        //additionally also store the the simulation result for the extended time series
-                        pExp->storeExtendedTimeSeriesData(pExp->getTimeData()[j]);
                       }
                     else
                       {