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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) |
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dict | track_generation_no_transition (self, float diffusion_coefficient, float hurst_exponent, int track_length, np.ndarray initials, int|float start_time) |
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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) |
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dict | track_generation_constant (self, int track_length, np.ndarray initials, int starting_time) |
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◆ __init__()
None SMS_BP.simulate_foci.Track_generator.__init__ |
( |
| self, |
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np.ndarray | list | cell_space, |
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int | float | cell_axial_range, |
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int | frame_count, |
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int | float | exposure_time, |
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int | float | interval_time, |
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int | float | oversample_motion_time ) |
◆ _convert_frame_to_time()
int SMS_BP.simulate_foci.Track_generator._convert_frame_to_time |
( |
| self, |
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int | frame ) |
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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, |
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int | time ) |
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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, |
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int | track_length, |
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np.ndarray | initials, |
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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, |
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float | diffusion_coefficient, |
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float | hurst_exponent, |
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int | track_length, |
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np.ndarray | initials, |
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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, |
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np.ndarray | list | diffusion_transition_matrix, |
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np.ndarray | list | hurst_transition_matrix, |
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np.ndarray | list | diffusion_parameters, |
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np.ndarray | list | hurst_parameters, |
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np.ndarray | list | diffusion_state_probability, |
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np.ndarray | list | hurst_state_probability, |
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int | track_length, |
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np.ndarray | initials, |
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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}
◆ 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: