SMS_BP
Single Molecule Simulations -BP
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SMS_BP.simulate_foci.Track_generator Class Reference

Public Member Functions

None __init__ (self, np.ndarray|list cell_space, int|float cell_axial_range, int frame_count, int|float exposure_time, int|float interval_time, int|float oversample_motion_time)
 
dict track_generation_no_transition (self, float diffusion_coefficient, float hurst_exponent, int track_length, np.ndarray initials, int|float start_time)
 
dict track_generation_with_transition (self, np.ndarray|list diffusion_transition_matrix, np.ndarray|list hurst_transition_matrix, np.ndarray|list diffusion_parameters, np.ndarray|list hurst_parameters, np.ndarray|list diffusion_state_probability, np.ndarray|list hurst_state_probability, int track_length, np.ndarray initials, int|float start_time)
 
dict track_generation_constant (self, int track_length, np.ndarray initials, int starting_time)
 

Public Attributes

 cell_space
 
 min_x
 
 max_x
 
 min_y
 
 max_y
 
 cell_axial_range
 
 space_lim
 
 frame_count
 
 exposure_time
 
 interval_time
 
 oversample_motion_time
 
 total_time
 

Protected Member Functions

int _convert_time_to_frame (self, int time)
 
int _convert_frame_to_time (self, int frame)
 

Constructor & Destructor Documentation

◆ __init__()

None SMS_BP.simulate_foci.Track_generator.__init__ ( self,
np.ndarray | list cell_space,
int | float cell_axial_range,
int frame_count,
int | float exposure_time,
int | float interval_time,
int | float oversample_motion_time )

Member Function Documentation

◆ _convert_frame_to_time()

int SMS_BP.simulate_foci.Track_generator._convert_frame_to_time ( self,
int frame )
protected
Parameters:
-----------
frame : int
    frame number

Returns:
--------
int: time in ms

◆ _convert_time_to_frame()

int SMS_BP.simulate_foci.Track_generator._convert_time_to_frame ( self,
int time )
protected
Parameters:
-----------
time : int
    time in ms

Returns:
--------
int: frame number

◆ track_generation_constant()

dict SMS_BP.simulate_foci.Track_generator.track_generation_constant ( self,
int track_length,
np.ndarray initials,
int starting_time )
Parameters:
-----------
track_length : int
    mean track length, in this case the track length is constant with this mean
initials : array-like
    [[x,y,z]] coordinates of the initial positions of the track
starting_time : int
    time at which the track start (this is not the frame, and needs to be converted to the frame using the exposure time and interval time and the oversample motion time)

Returns:
--------
np.ndarray
    track data for the constant track, {"xy":xyz,"frames":frames,"diffusion_coefficient":diffusion_coefficient,"hurst":hurst_exponent,"initial":initial}

◆ track_generation_no_transition()

dict SMS_BP.simulate_foci.Track_generator.track_generation_no_transition ( self,
float diffusion_coefficient,
float hurst_exponent,
int track_length,
np.ndarray initials,
int | float start_time )
Simulates the track generation with no transition between the diffusion coefficients and the hurst exponents
namely, this means each track has a unique diffusion coefficient and hurst exponent
This simulation is confined to the cell space and the axial range of the cell

Parameters:
-----------
diffusion_coefficient : float
    diffusion coefficient for the track
hurst_exponent : float
    hurst exponent for the track
track_length : int
    track_length for the track
initials : array-like
    [[x,y,z]] coordinates of the initial positions of the track
start_time : int
    time at which the track start (this is not the frame, and needs to be converted to the frame using the exposure time and interval time and the oversample motion time)
Returns:
--------
dict-like with format: {"xy":xyz,"frames":frames,"diffusion_coefficient":diffusion_coefficient,"hurst":hurst_exponent,"initial":initial}

◆ track_generation_with_transition()

dict SMS_BP.simulate_foci.Track_generator.track_generation_with_transition ( self,
np.ndarray | list diffusion_transition_matrix,
np.ndarray | list hurst_transition_matrix,
np.ndarray | list diffusion_parameters,
np.ndarray | list hurst_parameters,
np.ndarray | list diffusion_state_probability,
np.ndarray | list hurst_state_probability,
int track_length,
np.ndarray initials,
int | float start_time )
Genereates the track data with transition between the diffusion coefficients and the hurst exponents

Parameters:
-----------
diffusion_transition_matrix : array-like
    transition matrix for the diffusion coefficients
hurst_transition_matrix : array-like
    transition matrix for the hurst exponents
diffusion_parameters : array-like
    diffusion coefficients for the tracks
hurst_parameters : array-like
    hurst exponents for the tracks
diffusion_state_probability : array-like
    probabilities for the diffusion coefficients
hurst_state_probability : array-like
    probabilities for the hurst exponents
track_length : int
    track_length for the track
initials : array-like
    [[x,y,z]] coordinates of the initial positions of the track
start_time : int
    time at which the track start (this is not the frame, and needs to be converted to the frame using the exposure time and interval time and the oversample motion time)

Returns:
--------
dict-like with format: {"xy":xyz,"frames":frames,"diffusion_coefficient":diffusion_coefficient,"hurst":hurst_exponent,"initial":initial}

Member Data Documentation

◆ cell_axial_range

SMS_BP.simulate_foci.Track_generator.cell_axial_range

◆ cell_space

SMS_BP.simulate_foci.Track_generator.cell_space

◆ exposure_time

SMS_BP.simulate_foci.Track_generator.exposure_time

◆ frame_count

SMS_BP.simulate_foci.Track_generator.frame_count

◆ interval_time

SMS_BP.simulate_foci.Track_generator.interval_time

◆ max_x

SMS_BP.simulate_foci.Track_generator.max_x

◆ max_y

SMS_BP.simulate_foci.Track_generator.max_y

◆ min_x

SMS_BP.simulate_foci.Track_generator.min_x

◆ min_y

SMS_BP.simulate_foci.Track_generator.min_y

◆ oversample_motion_time

SMS_BP.simulate_foci.Track_generator.oversample_motion_time

◆ space_lim

SMS_BP.simulate_foci.Track_generator.space_lim

◆ total_time

SMS_BP.simulate_foci.Track_generator.total_time

The documentation for this class was generated from the following file: