/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    itkBioCellBase.cxx
  Language:  C++
  Date:      $Date$
  Version:   $Revision$

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#include "itkBioCellBase.h"
#include <new>

#include "vnl/vnl_math.h"
#include "vnl/vnl_sample.h"
#include "itkMath.h"

namespace itk {

namespace bio {
  
CellBase::ColorType    CellBase::DefaultColor;

double             CellBase::DefaultRadius         =        1.00; // microns

double             CellBase::GrowthRadiusIncrement =        0.01; // microns
double             CellBase::GrowthRadiusLimit     =        2.00; // microns

unsigned long      CellBase::MaximumGenerationLimit =        30L; // 30th generation 

unsigned long      CellBase::GrowthMaximumLatencyTime    =   50; 
unsigned long      CellBase::DivisionMaximumLatencyTime  =   50; 

double             CellBase::NutrientSelfRepairLevel  =       0; 
double             CellBase::EnergySelfRepairLevel    =       0; 

double             CellBase::DefaultEnergyIntake      =       1; 
double             CellBase::DefaultNutrientsIntake   =       1; 

unsigned long      CellBase::Counter = 0; // number of cells created

CellBase::GeneIdType   CellBase::RedGene   = "Red";
CellBase::GeneIdType   CellBase::GreenGene = "Green";
CellBase::GeneIdType   CellBase::BlueGene  = "Blue";
CellBase::GeneIdType   CellBase::Cdk2E     = "Cdk2E";
CellBase::GeneIdType   CellBase::Caspase   = "Caspase";
CellBase::GeneIdType   CellBase::Pressurin = "Pressurin";

double             CellBase::ChemoAttractantLowThreshold  = 200.0f;
double             CellBase::ChemoAttractantHighThreshold = 255.0f;

CellBase::ColorType    CellBase::WellNourishedColor;
CellBase::ColorType    CellBase::HopefullColor;
CellBase::ColorType    CellBase::StarvingColor;

/**
 *    Constructor Lonely Cell
 */ 
CellBase
::CellBase()
{

  m_Genome      = NULL;
  m_GenomeCopy  = NULL;
  
  m_Radius      = DefaultRadius;
  m_Color       = DefaultColor;
  
  m_Pressure  = 0.0f;

  m_ParentIdentifier = 0;    // Parent cell has to write here

  // The first Cell is numbered as 1
  Counter++;
  m_SelfIdentifier = Counter;  

  m_Generation     = 0;
  m_CycleState     = Gap1;  // cells are created in Gap1 state

  // Start with minimum reserves
  m_NutrientsReserveLevel = NutrientSelfRepairLevel + DefaultNutrientsIntake;
  m_EnergyReserveLevel    = EnergySelfRepairLevel   + DefaultEnergyIntake;

  // delay before starting to grow after Mitosis
  m_GrowthLatencyTime   = static_cast<unsigned long>( 
       vnl_sample_uniform( 0UL, this->GetGrowthMaximumLatencyTime()) );

  // add a random time before starting to grow
  m_DivisionLatencyTime = static_cast<unsigned long>(
      vnl_sample_uniform( 0, this->GetDivisionMaximumLatencyTime() ) );

  m_ScheduleApoptosis    = false;
  m_ChemoAttractantLevel = 200.0f;

  // too young to die...
  m_MarkedForRemoval = false;

}

/**
 *    Destructor   
 */ 
CellBase
::~CellBase()
{
  if( m_Genome )
    {
    delete m_Genome;
    m_Genome = NULL;
    }
  if( m_GenomeCopy )
    {
    delete m_GenomeCopy;
    m_GenomeCopy = NULL;
    }
}

/**
 *    DNA Replication 
 */ 
void
CellBase
::DNAReplication(void) 
{
  m_GenomeCopy = new GenomeType;
  m_GenomeCopy->Copy( *m_Genome );
}

/**
 *    Programmed Cell Death 
 *    This is the cellular equivalent of suicide.
 */ 
void
CellBase
::Apoptosis(void) 
{
  if( m_Genome )
    {
    delete m_Genome;
    m_Genome = NULL;
    }
  if( m_GenomeCopy )
    {
    delete m_GenomeCopy;
    m_GenomeCopy = NULL;
    }
}

/**
 *    Check point after division
 *    This check point will control
 *    the entrance in the growth stage.
 *    It returns true when conditions
 *    required for growth are satisfied.
 */ 
bool
CellBase
::CheckPointGrowth(void) 
{
  return true;
}

/**
 *    Check point before initiating DNA replication.
 *    This check point controls the entrance in the 
 *    duplication of the genome by DNA synthesis, also
 *    known as the S phase of the Cell cycle.
 *    This method returns true when conditions required 
 *    for DNA replication are satisfied.
 */ 
bool
CellBase
::CheckPointDNAReplication(void) 
{
  // radius & teleomerasa counting should be removed from here
  // and be related to Cdk expression by using proteins like P53
  // The radius should be estimated by a cytoskeleton-related protein.
  const bool fatality = (m_Generation < MaximumGenerationLimit );
  const bool radius   = (m_Radius >= GrowthRadiusLimit);


  bool isOkToReplicate = true;
  const double cdk2E = m_Genome->GetExpressionLevel( Cdk2E );
  if( cdk2E < 0.8 )
    {
    isOkToReplicate = false;
    }
  
  bool tooEarlyToReplicate = true;
  if( m_DivisionLatencyTime )
    {
    m_DivisionLatencyTime--;
    }
  else
    {
    tooEarlyToReplicate = false;
    }

  bool goodCellMatrix = false;
  if( !m_ScheduleApoptosis )
    {
    if( m_ChemoAttractantLevel > ChemoAttractantLowThreshold  &&
        m_ChemoAttractantLevel < ChemoAttractantHighThreshold    )
      {
      goodCellMatrix = true;
      }
    }


  return ( radius && fatality && isOkToReplicate && 
          !tooEarlyToReplicate && goodCellMatrix);
}

/**
 *    Check point before dividing the cell in two daughter cells
 *    at this point DNA replication has already been performed
 *    as well as DNA proofreading and error corrections. This 
 *    check point in principle shoult test if the resulting 
 *    genomes satisfy the quality standards of a living cell. 
 */
bool
CellBase
::CheckPointMitosis(void) 
{
  const bool DNAProofRead = ( m_GenomeCopy && m_Genome );
  if( !DNAProofRead ) 
  {
    std::cerr << "PANIC: DNA failed ! " << std::endl;
  }
  return DNAProofRead;
}

/**
 *    Check point before apoptosis
 *    This check point will control
 *    the entrance in the apoptosis stage.
 *    It returns true when conditions
 *    required for apoptosis are satisfied.
 *    The cell will die in apoptosis.
 */ 
bool
CellBase
::CheckPointApoptosis(void) 
{
  bool executeApoptosis;
  if(  m_Genome->GetExpressionLevel( Caspase ) > 0.8 )
    {
    executeApoptosis = true;
    }
  else
    {
    executeApoptosis = false;
    }
  return executeApoptosis;
}

/**
 *    Initialize common variables
 *    All this should go away once we setup Gene Networks for controlling the cell.
 */ 
void
CellBase
::Initialize(void) 
{
  CellBase::SetGrowthMaximumLatencyTime( 100 );
  CellBase::SetDivisionMaximumLatencyTime( 100 );

  CellBase::SetDefaultRadius( 1.0 );
  CellBase::SetGrowthRadiusIncrement( 0.01 );
  CellBase::SetGrowthRadiusLimit( 2.00 );
 
  SetMaximumGenerationLimit( 40 ); // it should use Teleomeres for implementing this

  WellNourishedColor.Set(    0.0f, 0.0f, 1.0f );
  HopefullColor.Set(         0.0f, 1.0f, 0.0f );
  StarvingColor.Set(         1.0f, 0.0f, 0.0f );

  SetDefaultColor( HopefullColor );

}

/**
 *  Mark this cell for removal
 *  The cellular aggregate with remove
 *  this cell from its list at the earliest occasion
 */ 
void
CellBase
::MarkForRemoval(void) 
{
  m_MarkedForRemoval = true;
}

/**
 *  Mark this cell for removal
 *  The cellular aggregate with remove
 *  this cell from its list at the earliest occasion
 */ 
bool
CellBase
::MarkedForRemoval(void) const
{
  return m_MarkedForRemoval;
}

/**
 *   Cell Growth
 *   Growth is conditioned to the availability of 
 *   nutrients and energy beyond the critical limit 
 *   of self-repair
 *   
 *   Growth is limited by a constraint in the size
 *   of cell's radius
 */ 
void
CellBase
::Grow(void) 
{
  if( m_GrowthLatencyTime )
  {
    m_GrowthLatencyTime--;
    return;
  }

  if ( m_NutrientsReserveLevel > NutrientSelfRepairLevel &&
       m_EnergyReserveLevel    > EnergySelfRepairLevel       )
    {
    m_Radius += GrowthRadiusIncrement;
    if( m_Radius > GrowthRadiusLimit )
      {
      m_Radius = GrowthRadiusLimit;
      }
    }
}

/**
 *    Set Growth Latency Time
 */ 
void
CellBase
::SetGrowthMaximumLatencyTime( unsigned long latency )
{
  CellBase::GrowthMaximumLatencyTime = latency;
}

/**
 *    Get Growth Latency Time
 */ 
unsigned long 
CellBase
::GetGrowthMaximumLatencyTime( void ) 
{
  return CellBase::GrowthMaximumLatencyTime;
}

/**
 *    Return the ID  of this cell
 */ 
CellBase::IdentifierType
CellBase
::GetSelfIdentifier(void) const
{
  return m_SelfIdentifier;
}

/**
 *    Return the ID  of the parent cell
 */ 
CellBase::IdentifierType
CellBase
::GetParentIdentifier(void) const
{
  return m_ParentIdentifier;
}

/**
 *    Return the radius 
 */ 
double
CellBase
::GetRadius(void) const
{
  return m_Radius;
}

/**
 *    Return the Color 
 */ 
CellBase::ColorType
CellBase
::GetColor(void) const
{
  return m_Color;
}

/**
 *    Set the value of the initial cell radius.
 */ 
void
CellBase
::SetDefaultRadius( double value ) 
{
  DefaultRadius = value;
}

/**
 *    Set the value of the limiting cell radius
 *    this is a static value used for the whole
 *    cellular aggregate
 */ 
void
CellBase
::SetGrowthRadiusLimit( double value ) 
{
  GrowthRadiusLimit = value;
}

/**
 *    Set the amount of Energy that is needed for Self-repair.
 *    Cells that go below this level will degrade and enter
 *    termination stage.
 */ 
void
CellBase
::SetEnergySelfRepairLevel( double value ) 
{
  EnergySelfRepairLevel = value;
}

/**
 *    Set the amount of Nutrients that are needed for Self-repair.
 *    Cells that go below this level will degrade and enter
 *    termination stage.
 */ 
void
CellBase
::SetNutrientSelfRepairLevel( double value ) 
{
  NutrientSelfRepairLevel = value;
}

/**
 *    Set the value of the limit of cell generation.
 *    After this generation cells will stop dividing
 *    A mechanism similar to the inhibition of Telomerase
 *    that impose a limit to the maximum number of times
 *    that the genome can be replicated.
 */ 
void
CellBase
::SetMaximumGenerationLimit( unsigned long generationLimit )
{
  MaximumGenerationLimit = generationLimit;
}

/**
 *    Get the value of the limiting cell radius
 *    this is a static value used for the whole
 *    cellular aggregate
 */ 
double
CellBase
::GetGrowthRadiusLimit( void ) 
{
  return GrowthRadiusLimit;
}

/**
 *    Set the value of the increment in cellular
 *    radius at each time step
 *    this is a static value used for the whole
 *    cellular aggregate
 */ 
void
CellBase
::SetGrowthRadiusIncrement( double value ) 
{
  GrowthRadiusIncrement = value;
}

/**
 *    Ingestion of nutrients
 */
void
CellBase
::NutrientsIntake(void) 
{
  m_NutrientsReserveLevel += DefaultNutrientsIntake;
}

/**
 *    Acquisition of energy
 */
void
CellBase
::EnergyIntake(void) 
{
  m_EnergyReserveLevel += DefaultEnergyIntake;
}

/**
 *   Compute the Gene Network
 *   This method update the level of expression of 
 *   all the genes in the cell's genome.
 *   see: http://www.ingeneue.org  for details
 */ 
void 
CellBase
::ComputeGeneNetwork(void) 
{
  // Default level of pigments
  m_Genome->SetExpressionLevel( CellBase::RedGene,   1.0 );
  m_Genome->SetExpressionLevel( CellBase::GreenGene, 1.0 );
  m_Genome->SetExpressionLevel( CellBase::BlueGene,  1.0 );


  // Color the cell acording to pressure.
  // This is done by generating pigments under 
  // the influence of presure.
  const double pressurinLevel = m_Genome->GetExpressionLevel( Pressurin );

  const double red = GenomeType::Sigmoide( 5.0, 1.0, pressurinLevel );

  m_Genome->SetExpressionLevel( RedGene,       red );
  m_Genome->SetExpressionLevel( BlueGene,  1.0-red );
  m_Genome->SetExpressionLevel( GreenGene,     0.0 );

 
  // Color the Cell acording to the substrate.
  // This is done by generating pigments.
  // This color overrides the selection of the Presure...

  if( m_ChemoAttractantLevel > ChemoAttractantHighThreshold )
    {
    m_Genome->SetExpressionLevel( RedGene,   WellNourishedColor.GetRed() );
    m_Genome->SetExpressionLevel( GreenGene, WellNourishedColor.GetGreen() );
    m_Genome->SetExpressionLevel( BlueGene,  WellNourishedColor.GetBlue() );
    }
  else if( m_ChemoAttractantLevel > ChemoAttractantLowThreshold )
    {
    m_Genome->SetExpressionLevel( RedGene,   HopefullColor.GetRed() );
    m_Genome->SetExpressionLevel( GreenGene, HopefullColor.GetGreen() );
    m_Genome->SetExpressionLevel( BlueGene,  HopefullColor.GetBlue() );
    }
  else
    {
    m_Genome->SetExpressionLevel( RedGene,   StarvingColor.GetRed() );
    m_Genome->SetExpressionLevel( GreenGene, StarvingColor.GetGreen() );
    m_Genome->SetExpressionLevel( BlueGene,  StarvingColor.GetBlue() );
    }


  // Prevent cells from replicating if they are in a high pressure zone
  const double cdk2E = GenomeType::Sigmoide( 2.0, -0.5, pressurinLevel );
  m_Genome->SetExpressionLevel( Cdk2E, cdk2E );
  
  // If the pressure is really high, then commit suicide
  const double caspase = GenomeType::Sigmoide( 3.0, 90.0, pressurinLevel );
  m_Genome->SetExpressionLevel( Caspase, caspase );


}

/**
 *   Secrete synthetized products resulting from 
 *   the gene network update
 */ 
void
CellBase
::SecreteProducts(void) 
{
  typedef ColorType::ValueType ColorValueType;

  m_Color.SetRed(   ColorValueType( m_Genome->GetExpressionLevel( RedGene   ) ) );
  m_Color.SetGreen( ColorValueType( m_Genome->GetExpressionLevel( GreenGene ) ) );
  m_Color.SetBlue(  ColorValueType( m_Genome->GetExpressionLevel( BlueGene  ) ) );
}

/**
 *    Set default Color
 */
void
CellBase
::SetDefaultColor( const ColorType & color )
{
  DefaultColor = color;
}

/**
 *    Reset the counter 
 */
void
CellBase
::ResetCounter( void )
{
  Counter = 0;
}

/**
 *    Set Division Latency Time
 */ 
void
CellBase
::SetDivisionMaximumLatencyTime( unsigned long latency )
{
  CellBase::DivisionMaximumLatencyTime = latency;
}

/**
 *    Get Division Latency Time
 */ 
unsigned long 
CellBase
::GetDivisionMaximumLatencyTime( void )
{
  return CellBase::DivisionMaximumLatencyTime;
}

/**
 *    Set ChemoAttractantLowThreshold
 */ 
void
CellBase
::SetChemoAttractantLowThreshold( double lowvalue )
{
  CellBase::ChemoAttractantLowThreshold = lowvalue;
}

/**
 *    Set ChemoAttractantHighThreshold
 */ 
void
CellBase
::SetChemoAttractantHighThreshold( double highvalue )
{
  CellBase::ChemoAttractantHighThreshold = highvalue;
}

}  // end namespace bio

}  // end namespace itk