ReparametrizationFunctionWrapper.cpp

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//
// File: ReparametrizationFunctionWrapper.h
// Created by: Julien Dutheil
// Created on: Fri Jan  30 09:30 2009
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)

   This software is a computer program whose purpose is to provide classes
   for numerical calculus.

   This software is governed by the CeCILL  license under French law and
   abiding by the rules of distribution of free software.  You can  use,
   modify and/ or redistribute the software under the terms of the CeCILL
   license as circulated by CEA, CNRS and INRIA at the following URL
   "http://www.cecill.info".

   As a counterpart to the access to the source code and  rights to copy,
   modify and redistribute granted by the license, users are provided only
   with a limited warranty  and the software's author,  the holder of the
   economic rights,  and the successive licensors  have only  limited
   liability.

   In this respect, the user's attention is drawn to the risks associated
   with loading,  using,  modifying and/or developing or reproducing the
   software by the user in light of its specific status of free software,
   that may mean  that it is complicated to manipulate,  and  that  also
   therefore means  that it is reserved for developers  and  experienced
   professionals having in-depth computer knowledge. Users are therefore
   encouraged to load and test the software's suitability as regards their
   requirements in conditions enabling the security of their systems and/or
   data to be ensured and,  more generally, to use and operate it in the
   same conditions as regards security.

   The fact that you are presently reading this means that you have had
   knowledge of the CeCILL license and that you accept its terms.
 */

#include "ReparametrizationFunctionWrapper.h"
#include "../../App/ApplicationTools.h"
#include <typeinfo>
using namespace bpp;
using namespace std;

void ReparametrizationFunctionWrapper::init_(bool verbose)
{
  for (size_t i = 0; i < functionParameters_.size(); i++)
  {
    Parameter& p = functionParameters_[i];
    Constraint* constraint = p.getConstraint();
    const string name = p.getName();
    double value = p.getValue();
    if (!constraint)
    {
      if (verbose)
        ApplicationTools::displayMessage("Parameter " + name + " does not need to be transformed.");
      addParameter_(new PlaceboTransformedParameter(name, value));
    }
    else
    {
      IntervalConstraint* interval = dynamic_cast<IntervalConstraint*>(constraint);
      if (interval) {
        bool isInfinite = (!interval->finiteLowerBound()) || (!interval->finiteUpperBound());
        if (!isInfinite)
        {
          if (!interval->strictLowerBound() && !interval->strictUpperBound())
          {
            // Case 1: [a,b]
            // This solves an issue if the original value is at the bound.
            double correctedValue = value;
            if (abs(value - interval->getLowerBound()) < NumConstants::TINY())
              correctedValue = interval->getLowerBound() + NumConstants::TINY();
            if (abs(value - interval->getUpperBound()) < NumConstants::TINY())
              correctedValue = interval->getUpperBound() - NumConstants::TINY();
            IntervalTransformedParameter* pp = new IntervalTransformedParameter(name, correctedValue, interval->getLowerBound(), interval->getUpperBound());
            addParameter_(pp);
            if (verbose)
              ApplicationTools::displayMessage("Parameter " + name + " was tanh transformed: " + TextTools::toString(value) + "->" + TextTools::toString(pp->getValue()));
          }
          else if (interval->strictLowerBound() && interval->strictUpperBound())
          {
            // Case 2: ]a,b[
            // We have to correct the bound in order to prevent numerical issues.
            // It can happens that the original bound is matched because of rounding errors.
            IntervalTransformedParameter* pp = new IntervalTransformedParameter(name, value, interval->getLowerBound() + NumConstants::TINY(), interval->getUpperBound() - NumConstants::TINY());
            addParameter_(pp);
            if (verbose)
              ApplicationTools::displayMessage("Parameter " + name + " was tanh transformed: " + TextTools::toString(value) + "->" + TextTools::toString(pp->getValue()));
          }
          else if (!interval->strictLowerBound() && interval->strictUpperBound())
          {
            // Case 3: [a,b[
            // This solves an issue if the original value is at the bound.
            double correctedValue = value;
            if (abs(value - interval->getLowerBound()) < NumConstants::TINY())
              correctedValue = interval->getLowerBound() + NumConstants::TINY();
            IntervalTransformedParameter* pp = new IntervalTransformedParameter(name, correctedValue, interval->getLowerBound(), interval->getUpperBound() - NumConstants::TINY());
            addParameter_(pp);
            if (verbose)
              ApplicationTools::displayMessage("Parameter " + name + " was tanh transformed: " + TextTools::toString(value) + "->" + TextTools::toString(pp->getValue()));
          }
          else if (interval->strictLowerBound() && !interval->strictUpperBound())
          {
            // Case 4: ]a,b]
            // This solve an issue if the original value is at the bound.
            double correctedValue = value;
            if (abs(value - interval->getUpperBound()) < NumConstants::TINY())
              correctedValue = interval->getUpperBound() - NumConstants::TINY();
            IntervalTransformedParameter* pp = new IntervalTransformedParameter(name, correctedValue, interval->getLowerBound() + NumConstants::TINY(), interval->getUpperBound());
            addParameter_(pp);
            if (verbose)
              ApplicationTools::displayMessage("Parameter " + name + " was tanh transformed: " + TextTools::toString(value) + "->" + TextTools::toString(pp->getValue()));
          }
        }
        else
        {
          if (interval->strictLowerBound() && !interval->finiteUpperBound())
          {
            // Case 5: ]a, +inf[
            RTransformedParameter* pp = new RTransformedParameter(name, value, interval->getLowerBound() + NumConstants::TINY(), true);
            addParameter_(pp);
            if (verbose)
              ApplicationTools::displayMessage("Parameter " + name + " was log transformed: " + TextTools::toString(value) + "->" + TextTools::toString(pp->getValue()));
          }
          else if (!interval->strictLowerBound() && !interval->finiteUpperBound())
          {
            // Case 6: [a, +inf[
            // This solve an issue if the original value is at the bound.
            double correctedValue = value;
            if (abs(value - interval->getLowerBound()) < NumConstants::TINY())
              correctedValue = interval->getLowerBound() + NumConstants::TINY();
            RTransformedParameter* pp = new RTransformedParameter(name, correctedValue, interval->getLowerBound(), true);
            addParameter_(pp);
            if (verbose)
              ApplicationTools::displayMessage("Parameter " + name + " was log transformed: " + TextTools::toString(value) + "->" + TextTools::toString(pp->getValue()));
          }
          else if (!interval->finiteLowerBound() && interval->strictUpperBound())
          {
            // Case 7: ]-inf, a[
            RTransformedParameter* pp = new RTransformedParameter(name, value, interval->getUpperBound() - NumConstants::TINY(), false);
            addParameter_(pp);
            if (verbose)
              ApplicationTools::displayMessage("Parameter " + name + " was log transformed: " + TextTools::toString(value) + "->" + TextTools::toString(pp->getValue()));
          }
          else if (!interval->finiteLowerBound() && !interval->strictUpperBound())
          {
            // Case 8: ]-inf, a]
            // This solve an issue if the original value is at the bound.
            double correctedValue = value;
            if (abs(value - interval->getUpperBound()) < NumConstants::TINY())
              correctedValue = interval->getUpperBound() - NumConstants::TINY();
            RTransformedParameter* pp = new RTransformedParameter(name, correctedValue, interval->getUpperBound(), false);
            addParameter_(pp);
            if (verbose)
              ApplicationTools::displayMessage("Parameter " + name + " was log transformed: " + TextTools::toString(value) + "->" + TextTools::toString(pp->getValue()));
          }
        }
      }
      else
      {
        // Nothing found
        if (verbose)
        {
          ApplicationTools::displayWarning("No transformation found for this constraint '" + constraint->getDescription() + "'! Parameter " + p.getName());
        }
        addParameter_(new PlaceboTransformedParameter(name, value));
      }
    }
  }
}

void ReparametrizationFunctionWrapper::fireParameterChanged(const ParameterList& parameters)
{
  // Recompute function parameters:
  // We could update only the parameter that actually changed,
  // but that would implied a quick sort on parameter names (nlog(n))
  // whereas using a loop over the set is in o(n). It should hence be
  // more efficient in most cases.
  for (size_t i = 0; i < getNumberOfParameters(); ++i)
  {
    double x = dynamic_cast<TransformedParameter&>(getParameter_(i)).getOriginalValue();
    try
    {
      functionParameters_[i].setValue(x);
    }
    catch (ConstraintException& ce)
    {
      (*ApplicationTools::error << "Oups, value " << x << " led to a constraint exception. The transformed value was " << getParameter_(i).getValue()).endLine();
      throw ce;
    }
  }
}