k-Wave Toolbox

 

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Functions — By Category

  Alphabetical List
Wave Propagation Simulate time-domain acoustic wave fields
Image Reconstruction Photoacoustic image reconstruction
Geometry Creation Geometry and shape creation
Acoustic Absorption Absorption coefficient calculation and conversion
Grid and Matrix Utilities Grid and matrix utilities
Filtering and Spectral Utilities Filtering, windowing, and spectral analysis utilities
Display and Visualisation Display and visualise data
Ultrasound Utilities Creation and processing of ultrasound signals
HDF5 Utilities Write and read HDF5 input and output files used for the C++ code
Other Utilities System parameters and utilities

Wave Propagation

kspaceFirstOrder1D 1D time-domain simulation of wave propagation
kspaceFirstOrder2D 2D time-domain simulation of wave propagation
kspaceFirstOrder3D 3D time-domain simulation of wave propagation
kspaceFirstOrder3DC 3D time-domain simulation of wave propagation using C++ code
kspaceFirstOrder3DG 3D time-domain simulation of wave propagation on a GPU using C++ CUDA code
kspaceSecondOrder Fast time-domain simulation of wave propagation for homogeneous media
mendousse Compute Mendousse's solution for nonlinear wave propagation in viscous media
pstdElastic2D 2D time-domain simulation of elastic wave propagation
pstdElastic3D 3D time-domain simulation of elastic wave propagation

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Image Reconstruction

kspaceLineRecon 2D linear FFT reconstruction
kspacePlaneRecon 3D planar FFT reconstruction

See also kspaceFirstOrder1D, kspaceFirstOrder2D, and kspaceFirstOrder3D for time-reversal image reconstruction

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Geometry Creation

makeBall Create a binary map of filled ball within a 3D grid
makeCartCircle Create a 2D Cartesian circle or arc
makeCartSphere Create a 3D Cartesian sphere
makeCircle Create a binary map of a circle within a 2D grid
makeDisc Create a binary map of a filled disc within a 2D grid
makeLine Create a binary map of a straight line within a 2D grid
makeSphere Create a binary map of a sphere within a 3D grid
makeSphericalSection Create a binary map of a sphere segment within a 3D grid

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Acoustic Absorption

attenComp Attenuation compensation using time-variant filtering
attenuationWater Calculate ultrasound attenuation in distilled water
db2neper Convert decibels to nepers
fitPowerLawParams Fit power law absorption parameters for highly absorbing media
neper2db Convert nepers to decibels
powerLawKramersKronig Calculate dispersion for power law absorption

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Grid and Matrix Utilities

cart2grid Interpolate a set of Cartesian points onto a binary grid
expandMatrix Enlarge a matrix by extending the edge values
findClosest Return the closest value in a matrix
grid2cart Return the Cartesian coordinates of the non-zero points of a binary grid
interpCartData Interpolate data from a Cartesian to a binary sensor mask
interpftn Resample data using Fourier interpolation
loadImage Load an image file
makeGrid Create k-Wave grid structure
maxND Return the value and indices of the largest value in an N-D array
minND Return the value and indices of the smallest value in an N-D array
numDim Return the number of matrix dimensions
resize Resize a matrix
reorderSensorData Reorder sensor data from kspaceFirstOrder2D based on angle
revolve2D Form 3D matrix from revolution of 2D matrix
timeShift Shift time series to and from staggered temporal grid
unmaskSensorData Reorder data recorded using a binary sensor mask

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Filtering and Spectral Utilities

applyFilter Filter input with low, high, or band pass filter
envelopeDetection Extract signal envelope using the Hilbert Transform
filterTimeSeries Filter signal using the Kaiser windowing method
gaussianFilter Filter signals using a frequency domain Gaussian filter
getAlphaFilter Create filter for medium.alpha_filter
getBLI Compute underlying Fourier band-limited interpolant (BLI)
getFDMatrix Create a matrix of finite-difference coefficients
getWin Return a frequency domain windowing function
gradientFD Calculate the gradient using a finite-difference method
gradientSpect Calculate the gradient using a Fourier spectral method
sharpness Calculate image sharpness metric
spect Compute the single sided amplitude and phase spectrums
smooth Smooth a matrix
vesselFilter Frangi's 3D vessel filter

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Display and Visualisation

beamPlot Plot volumetric data using intersecting planes
flyThrough Display a three-dimensional matrix slice by slice
getColorMap Return default k-Wave color map
overlayPlot Overlay two images
saveTiffStack Save volume data as a tiff stack
scaleFig Resize current figure window
stackedPlot Stacked linear plot
voxelPlot 3D plot of voxels in a binary matrix

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Ultrasound Utilities

envelopeDetection Extract signal envelope using the Hilbert Transform
focus Create input signal based on source mask and focus position
gaussianFilter Filter signals using a frequency domain Gaussian filter
hounsfield2density Convert Hounsfield units to density
logCompression Log compress an input signal
makeTransducer Create k-Wave ultrasound transducer
scanConversion Convert scan-lines in polar coordinates to a B-mode ultrasound image
toneBurst Create an enveloped single frequency tone burst

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HDF5 Utilities

h5compare Compare the contents of two HDF5 files
writeAttributes Write attributes to a k-Wave HDF5 file
writeFlags Write input flags to a k-Wave HDF5 file
writeGrid Write grid and PML properties to a k-Wave HDF5 file
writeMatrix Write MATLAB matrix to a k-Wave HDF5 file

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Other Utilities

addNoise Add Gaussian noise to a signal for a given SNR
benchmark Run performance benchmark
checkFactors Return the maximum prime factor for a range of numbers
checkStability Return maximum stable time step for k-space models
fwhm Compute the full width at half maximum
gaussian Create a Gaussian distribution
getDateString Create a string of the current date and time
getkWavePath Return pathname to the k-Wave Toolbox
getSpacedPoints Create vector of log or linear spaced points
makeTime Create an evenly spaced array of time points
scaleSI Scale a number to nearest SI unit prefix
scaleTime Convert seconds to hours, minutes, and seconds
speedSoundWater Calculate the speed of sound in water with temperature

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Running K-Sim On The GPU  Simulations In Three Dimensions   Functions — Alphabetical List Functions — Alphabetical List

© 2009-2014 Bradley Treeby and Ben Cox.