StateSystem¶
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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¶
Constructors¶
StateSystem¶
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public
StateSystem
(int N_states, double[][][] M_scaling)¶ Initialize the state system.
Parameters: - N_states – number of states
- 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¶
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public final double
getMeanTransitionLifetime
(int from, int to)¶ Parameters: - from – index of initial state
- to – index of final state
Returns: mean transition lifetime from one state to another
getTransitionRate¶
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public final double
getTransitionRate
(int from, int to)¶ Parameters: - from – index of initial state
- to – index of final state
Returns: transition rate from one state to another
isBleachedState¶
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public boolean
isBleachedState
(int state)¶ Returns true if the state is the bleached state (the last state of the model)
Parameters: - state – id of current state
Returns: state == (N_states - 1)
isOnState¶
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public boolean
isOnState
(int state)¶ Returns true if the state is the active state (the 0-th state)
Parameters: - state – id of current state
Returns: (state==0)
recalculate_lifetimes¶
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public final void
recalculate_lifetimes
(double laser_power)¶ 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.
Parameters: - laser_power – illumination intensity I to recalculate for