Description¶

job_finished.m¶

Functionality This function is used to interact with JobAllocator. At the end of a certain job, the thread can use this function to signal to JobAllocator that the task has been accomplished.

Note

Due to a problem with the API, this method is currently implemented by writing an empty file, whose name is the signal to be sent to JobAllocator (JobAllocator then scans for these files.)

Input

res_path:	(string) Directory where the message files to Job Allocator are written
thread_id:	(string) ID of the current thread

main.m¶

Functionality Main function of the ultrasound simulation routine (built mainly on top
of the FieldII US simulation program). When using this program in a distributed
setting, make sure you are using it in compiled mode, as it requires no MATLAB
licence.
This function takes in some configuration flags which setup the running mode of
the simulator. Mainly, they determine whether to run in data generation
mode, or scatterer generation mode. In the former, random pairs of
{scatter-map; b-mode image} are generated. In the latter, bmode images
are simulated for predefined scatterers. After configuring the simulator,
it enters an infinite loop where it requests simulation tasks from JobAllocator,
then runs them.

Input

thread_id:	(string) ID of the current thread. This can be passed as the first command line argument when running in compiled mode

make_cyst.m¶

Functionality This function creates a cyst scatter map. It is a circular inclusion of lesser amplitude.

Input

evaluation_mode:
opts:	Options structure for this simulation
fast_run:	Flag. Used in debugging for running the US simulation quickly
	Flag. If true, means the program is in evaluation mode, else in dataset generation mode.
sim2d:	Flag. If true, indicates the program is a 2D simulation (not 3D)
new_scatmap:	Flag. If true, indicates that a new random scatter-map can be generated.

Output

x_s:	Vector of x-coordinates of the scatterers
y_s:	Vector of y-coordinated of the scatterers
z_s:	Vector of z_coordinated of the scatterers
amplitudes:	Vector of amplitudes of the scatterers

make_ellipsoids.m¶

Functionality This function takes a regular 3D grid of points, and assigns them amplitudes. It does this by creating randomly-sized and rotated ellipsoids in that 3D space. The distance from the center of these ellipsoids describes a random spatial gradient. This spatial gradient is then used to assign amplitudes to the points in space.

Input

opts:	Options structure for this simulation.
x_size:	Lateral size of the phantom
y_size:	Elevation size of the phantom
z_size:	Axial size of the phantom
z_start:	Distance of the phantom from the transducer
x_g:	Vector of x_coordinates of the points of the input grid
y_g:	Vector of y_coordinates of the points of the input grid
z_g:	Vector of z_coordinates of the points of the input grid

Output :multiplicative_amplitude : Vector of amplitudes assigned to the points of the input 3D grid

make_image.m¶

Functionality This function takes a number of RF lines, places them together, and performs some additional processing to extract a B-mode image, or an RF-image, and saves them.

Input

opts:	Options structure for this simulation
probe_angle:	Angle in radians of US beam incidence
y_slice:	Depth of the current slice when simulating a 3D volume
render_bmode:	Flag: if true, renders a bmode image, else renders RF image

make_phantom.m¶

Functionality This function creates randomly placed scatterers (scatter map), as well as the amplitude associated with each scatterer to create a US phantom.

Input

evaluation_mode:
opts:	Options structure for this simulation
fast_run:	Flag. Used in debugging for running the US simulation quickly
	Flag. If true, means the program is in evaluation mode, else in dataset generation mode.
sim2d:	Flag. If true, indicates the program is a 2D simulation (not 3D)
new_scatmap:	Flag. If true, indicates that a new random scatter-map can be generated.

Output

generate_from_ct:
x_s:	Vector of x-coordinates of the scatterers
y_s:	Vector of y-coordinated of the scatterers
z_s:	Vector of z_coordinated of the scatterers
amplitudes:	Vector of amplitudes of the scatterers
	Flag. Whether to use CT images, or the method of random ellipsoids for scatter map generation.

optsInit.m¶

Functionality This function is where all the simulation settings, probe parameters, files, directories, and various other options for the FieldII simulator, and the phantom generation procedure are set.

Input

override_angles:
name:	(String). Name of the current experiment. An experiment is defined as all the different simulation settings of one particular phantom.
sim2d:	Flag. If true, indicates the program is a 2D simulation (not 3D)
	Flag. If true, indicates that the simulation angle is given in experiment name

Output

opts:	Options structure for this simulation

plotPhantom.m¶

Functionality This function plots US scatter pattern phantom, or saves it as image

Input

:pos : Positions of scatterers. This is a matrix of phantom scatterer positions (X,Y,Z) :amp : Scatterer amplitudes. This is a vector of phantom scatterer amplitudes (same number as entries in Phantom positions) :x_size : Width of phantom [mm] :z_size : Height of phantom [mm] :z_start : Start of phantom surface [mm] :titl : Plot title :exper : Experiment directory

request_job_new.m¶

Functionality This function sends a request to JobAllocator for a new simulation job. It parses the answer from JobAllocator to extract the details about the simulation job to be run, and stores this configuration in a struct called job.

Input :res_path : (string) Directory where the message files to Job Allocator are written :thread_id: (string) ID of the current thread

Output

job:	job struct containg a description of the allocated simulation job.

sample_from_ct.m¶

Functionality This function takes a regular 3D grid of points, and assigns them amplitudes. It does this by sampling existing medical image data (CT).

Input

opts:	Options structure for this simulation.
x_size:	Lateral size of the phantom
y_size:	Elevation size of the phantom
z_size:	Axial size of the phantom
z_start:	Distance of the phantom from the transducer
x_g:	Vector of x_coordinates of the points of the input grid
y_g:	Vector of y_coordinates of the points of the input grid
z_g:	Vector of z_coordinates of the points of the input grid

Output :multiplicative_amplitude : Vector of amplitudes assigned to the points of the input 3D grid

sim_img.m¶

Functionality This function takes a 3D scatter map, and rotates or translates it to simulate the positioning of the US probe relative to the scatter map. It then launches the simulation of the RF line specified by JobAllocator.

Input

opts:	Options structure for this simulation
probe_angle:	Angle in radians of US beam incidence
rf_line:	The number of the RF-line to be simulated
y_slice:	Depth of the current slice when simulating a 3D volume
amplitudes:	Vector of amplitudes of the scatterers in the scatter map
x:	Vector of x-coordinates of the scatterers
y:	Vector of y-coordinated of the scatterers
z:	Vector of z_coordinated of the scatterers

simulate_rf_line.m¶

Functionality This function is in charge of simulating a single RF line.

Input

opts:	Options structure for this simulation
probe_angle:	Angle in radians of US beam incidence
line_no:	The number of the RF-line to be simulated
amplitudes:	Vector of amplitudes of the scatterers in the scatter map
positions:	A N-by-3 matrix of the (x,y,z) coordinates of the N scatterers
y_slice:	Depth of the current slice when simulating a 3D volume

Output

Tx_aperture:	FieldII probe setting (Receive Aperture)
Rx_aperture:	FieldII probe setting (Transmit Aperture)

simulation_routine.m¶

Functionality This function reads the type of task which has been allocated (t1, t2, or t3), and acts accordingly.

t1: Generation of tissue phantoms

t2: Simulation of US interaction with tissue phantoms (scatter maps)

t3: US b-mode image creation from the simulated data

Input

evaluation_mode:
simulate:	Flag. Used to decide whether to simulate images or not. Used in debugging to see the result of scatter map generation without simulating its interaction with US
fast_run:	Flag. Used in debugging for running the US simulation quickly
	Flag. If true, means the program is in evaluation mode, else in dataset generation mode.
sim2d:	Flag. If true, indicates the program is a 2D simulation (not 3D)
new_scatmap:	Flag. If true, indicates that a new random scatter-map can be generated.
render_images:	Flag. If true, indicates whether to render the images or not.
job:	job struct containg a description of the allocated simulation job.
override_angles:
	Flag. If true, indicates that the simulation angle is given in experiment name
generate_incl:	Flag. This is a special mode. When set to true, the program generates a scatter map of a circular inclusion
generate_from_ct:
	Flag. Whether to use CT images, or the method of random ellipsoids for scatter map generation.