.. java:import:: java.io Serializable

StateSystem
===========

.. java:package:: ch.epfl.leb.sass.models.photophysics
   :noindex:

.. java:type:: public class StateSystem implements Serializable

   Class which describes a Markovian fluorophore state model. This class provides transition rates and mean lifetimes for Markovian models based on current laser illumination intensity.

   :author: stefko

Fields
------
current_laser_power
^^^^^^^^^^^^^^^^^^^

.. java:field:: protected double current_laser_power
   :outertype: StateSystem

   Laser power value for which the currently stored lifetime values are calculated.

Constructors
------------
StateSystem
^^^^^^^^^^^

.. java:constructor:: public StateSystem(int N_states, double[][][] M_scaling)
   :outertype: StateSystem

   Initialize the state system.

   :param N_states: number of states
   :param M_scaling: double[][][] matrix of dimensions N x N x A. A can be different for each position in the matrix. This matrix can be interpreted as follows: double[] P = M_scaling[i][j]; k_ij(I) = P[0] + P[1]*I + P[2]*I^2 + ... P[n]*I^n; k_ij(I) is transition rate between i-th and j-th state under laser illumination intensity I. The first row of this matrix is considered the active state, the last row is considered the bleached state.

Methods
-------
getMeanTransitionLifetime
^^^^^^^^^^^^^^^^^^^^^^^^^

.. java:method:: public final double getMeanTransitionLifetime(int from, int to)
   :outertype: StateSystem

   :param from: index of initial state
   :param to: index of final state
   :return: mean transition lifetime from one state to another

getNStates
^^^^^^^^^^

.. java:method:: public int getNStates()
   :outertype: StateSystem

   :return: number of states of this model

getTransitionRate
^^^^^^^^^^^^^^^^^

.. java:method:: public final double getTransitionRate(int from, int to)
   :outertype: StateSystem

   :param from: index of initial state
   :param to: index of final state
   :return: transition rate from one state to another

isBleachedState
^^^^^^^^^^^^^^^

.. java:method:: public boolean isBleachedState(int state)
   :outertype: StateSystem

   Returns true if the state is the bleached state (the last state of the model)

   :param state: id of current state
   :return: state == (N_states - 1)

isOnState
^^^^^^^^^

.. java:method:: public boolean isOnState(int state)
   :outertype: StateSystem

   Returns true if the state is the active state (the 0-th state)

   :param state: id of current state
   :return: (state==0)

recalculate_lifetimes
^^^^^^^^^^^^^^^^^^^^^

.. java:method:: public final void recalculate_lifetimes(double laser_power)
   :outertype: StateSystem

   Recalculates each element of the transition matrix, based on the scaling matrix provided at initialization. double[] P = M_scaling[i][j]; k_ij(I) = P[0] + P[1]*I + P[2]*I^2 + ... P[n]*I^n; k_ij(I) is transition rate between i-th and j-th state under laser illumination intensity I.

   :param laser_power: illumination intensity I to recalculate for