k-Wave Toolbox |

# 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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© 2009-2014 Bradley Treeby and Ben Cox.