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                                  k-Wave

                    A MATLAB toolbox for the time-domain 
                     simulation of acoustic wave fields
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VERSION INFORMATION
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Version 1.2, Released 28th August 2017
Written by Bradley Treeby, Ben Cox, and Jiri Jaros
See individual files for complete list of authors

Tested using:
   Windows 10 64-bit: MATLAB R2010a through to R2017a
   MacOS Sierra: MATLAB R2016b
   Linux Ubuntu 16.04: MATLAB R2016b

Please report bugs and suggestions on http://www.k-wave.org/forum
The toolbox may be downloaded from http://www.k-wave.org/download.php

NOTE: The photoacoustic reconstruction functions kspaceLineRecon and 
kspacePlaneRecon (all toolbox versions) do not work with R2012b.
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PRODUCT OVERVIEW
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k-Wave is an open source MATLAB toolbox designed for the time-domain 
simulation of propagating acoustic waves in 1D, 2D, or 3D [1]. The toolbox
has a wide range of functionality, but at its heart is an advanced numerical
model that can account for both linear and nonlinear wave propagation, an 
arbitrary distribution of heterogeneous material parameters, and power law 
acoustic absorption.

The numerical model is based on the solution of three coupled first-order 
partial differential equations which are equivalent to a generalised form 
of the Westervelt equation [2]. The equations are solved using a k-space 
pseudospectral method, where spatial gradients are calculated using a 
Fourier collocation scheme, and temporal gradients are calculated using a
k-space corrected finite-difference scheme. The temporal scheme is exact in
the limit of linear wave propagation in a homogeneous and lossless medium, 
and significantly reduces numerical dispersion in the more general case.

Power law acoustic absorption is accounted for using a linear integro-
differential operator based on the fractional Laplacian [3]. A split-field 
perfectly matched layer (PML) is used to absorb the waves at the edges of 
the computational domain. The main advantage of the numerical model used in 
k-Wave compared to models based on finite-difference time domain (FDTD) 
schemes is that fewer spatial and temporal grid points are needed for 
accurate simulations. This means the models run faster and use less memory. 
A detailed description of the model is given in the k-Wave User Manual and 
the references below.

[1] B. E. Treeby and B. T. Cox, "k-Wave: MATLAB toolbox for the simulation 
and reconstruction of photoacoustic wave-fields," J. Biomed. Opt., vol. 15,
no. 2, p. 021314, 2010. 
[2] B. E. Treeby, J. Jaros, A. P. Rendell, and B. T. Cox, "Modeling 
nonlinear ultrasound propagation in heterogeneous media with power law 
absorption using a k-space pseudospectral method," J. Acoust. Soc. Am., 
vol. 131, no. 6, pp. 4324-4336, 2012.
[3] B. E. Treeby and B. T. Cox, "Modeling power law absorption and 
dispersion for acoustic propagation using the fractional Laplacian," J. 
Acoust. Soc. Am., vol. 127, no. 5, pp. 2741-2748, 2010.
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INSTALLATION INSTRUCTIONS
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The k-Wave toolbox is installed by adding the root k-Wave folder to the 
MATLAB path. This can be done using the "Set Path" dialog box which is 
accessed by typing "pathtool" at the MATLAB command line. This dialog box 
can also be accessed using the "Set Path" button on the ribbon bar. Once the
dialog box is open, the toolbox is installed by clicking "Add Folder", 
selecting the k-Wave toolbox folder, and clicking "save". The toolbox can be
uninstalled in the same fashion. 

For Linux users, using the "Set Path" dialog box requires write access to 
pathdef.m. This file can be found under <...matlabroot...>/toolbox/local. To
find where MATLAB is installed, type "matlabroot" at the MATLAB command line.

Alternatively, the toolbox can be installed by adding the line 

    addpath('<...pathname...>/k-Wave');
    
to the startup.m file, where <...pathname...> is replaced with the location 
of the toolbox, and the slashes should be in the direction native to your 
operating system. If no startup.m file exists, create one, and save it in 
the MATLAB startup directory. 

After installation, restart MATLAB. You should then be able to see the 
k-Wave help files in the MATLAB help browser. This can be accessed by 
selecting "k-Wave Toolbox" from the contents page. Try selecting one of the
examples and then clicking "run the file". 

If you can't see "k-Wave Toolbox" in the contents list of the MATLAB help 
browser, try typing "help k-Wave" at the command prompt to see if the 
toolbox has been installed correctly. If it has and you still can't see the
help files, open "Preferences" and select "Help" and make sure "k-Wave 
Toolbox" or "All Products" is checked. 

After installation, to make the k-Wave documentation searchable from within
the MATLAB help browser, run

    builddocsearchdb(`<...pathname...>/k-Wave/helpfiles');
    
again using the slash direction native to your operating system. Note, the
created database file will only work with the version of MATLAB used to 
create it.

If using the C++ or CUDA versions of kspaceFirstOrder3D, the appropriate 
binaries (and library files if using Windows) should also be downloaded 
from http://www.k-wave.org/download.php and placed in the root "binaries"
folder of the toolbox.
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RELEASE NOTES
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New Features and Changes:
- thermal simulations are now supported using the kWaveDiffusion class and 
  bioheatExact
- focused bowl transducers can be created using makeArc and makeMultiArc in
  2D, and makeBowl and makeMultiBowl in 3D
- a warning is printed if dimension sizes have high prime factors
- default HDF5 compression level is now 0 (increases speed of saving input
  file for C++ codes)
- the compression level for HDF5 files can be set using the optional input
  'HDFCompressionLevel'
- movies are now saved using VideoWriter (see help for changes to optional 
  inputs)
- kspaceFirstOrder3DG now allows the device number of the GPU to be selected
- hounsfield2density now returns matrices of the same data type as the input
- kWaveGrid is now implemented as a handle class (only handles are passed to
  functions to save memory)
- kWaveGrid now returns wavenumber vectors for discrete cosine and sine 
  transforms
- writeMatrix now accepts an optional compression level input
- makeGrid has been deprecated, with grids created using the syntax 
  kgrid = kWaveGrid(...)
- makeTime has been deprecated, and is now a method of kWaveGrid
- makeTransducer has been deprecated, with transducers created using the 
  syntax transducer = kWaveTransducer(...)
- update to overlayPlot to allow optional inputs
- scaleSI now returns no scale for zero values
- makeCircle now supports circles not contained within the grid
- speedSoundWater now checks temperature limits
- update to style used in MATLAB documentation

Bug Fixes:
- bug fix in kspaceFirstOrder1D, kspaceFirstOrder2D, and kspaceFirstOrder3D
  for nonlinear simulations (convective nonlinearity term implemented 
  incorrectly)
- bug fix in using simulation functions in MATLAB 2016b and later (error 
  with use of nargin and nargout in subscripts)
- bug fix in kspaceFirstOrder2D when using sensor.directivity_pattern = 
  'gradient' (directional response incorrect)
- bug fix in kspaceFirstOrder3DG when using a sensor mask defined by
  opposing corners and recording intensity (generated error)
- bug fix in kspaceFirstOrder3D-OMP when using a kWaveTransducer source with
  checkpoint restart (wrong index used for time signal on restart)
- bug fix in kspaceLineRecon and kspacePlaneRecon (incorrect use of fftshift
  caused energy loss at certain frequencies)
- bug fix in findClosest (returned correct index but incorrect closest
  value)
- bug fix in setting apodization in kWaveTransducer class with only one 
  active element (returned NaN)
- bug fix in writeGrid for odd dimension sizes (used even wavenumber 
  components)

New Functions:
- bioheatExact
- createCWSignals
- extractAmpPhase
- focusedBowlONeil
- fourierShift
- getComputerInfo
- kWaveDiffusion
- makeArc
- makeMultiArc
- makeBowl
- makeMultiBowl

Deprecated Functions:
- makeGrid
- makeTime
- makeTransducer
- timeShift

New Examples:
- Example: Heat Diffusion In A Homogeneous Medium
- Example: Constant Rate Of Heat Deposition
- Example: Using A Binary Sensor Mask
- Example: Heating By A Focused Ultrasound Transducer
- Example: Iterative Image Reconstruction Using The Adjoint
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LICENSE
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k-Wave (c) 2009-2017 Bradley Treeby, Ben Cox, and Jiri Jaros (see individual
files for list of authors).

The k-Wave toolbox is distributed by the copyright owners under the terms of
the GNU Lesser General Public License (LGPL) which is a set of additional 
permissions added to the GNU General Public License (GPL). The full text of 
both licenses is included with the toolbox in the folder 'license'.

The licence places copyleft restrictions on the k-Wave toolbox. Essentially,
anyone can use the software for any purpose (commercial or non-commercial), 
the source code for the toolbox is freely available, and anyone can 
redistribute the software (in its original form or modified) as long as the
distributed product comes with the full source code and is also licensed 
under the LGPL. You can make private modified versions of the toolbox 
without any obligation to divulge the modifications so long as the modified
software is not distributed to anyone else. The copyleft restrictions only 
apply directly to the toolbox, but not to other (non-derivative) software 
that simply links to or uses the toolbox. 

k-Wave is distributed in the hope that it will be useful, but WITHOUT ANY 
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 
FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
details (http://www.gnu.org/licenses/lgpl.html). 

If you find the toolbox useful for your academic work, please consider 
citing one or more of the following papers:

1. Overview of the toolbox with applications in photoacoustics:

   B. E. Treeby and B. T. Cox, "k-Wave: MATLAB toolbox for the simulation  
   and reconstruction of photoacoustic wave-fields," J. Biomed. Opt., vol. 
   15, no. 2, p. 021314, 2010.

2. Nonlinear ultrasound model and the C++ code:

   B. E. Treeby, J. Jaros, A. P. Rendell, and B. T. Cox, "Modeling nonlinear 
   ultrasound propagation in heterogeneous media with power law absorption 
   using a k-space pseudospectral method," J. Acoust. Soc. Am., vol. 131, 
   no. 6, pp. 4324-4336, 2012. 

3. Elastic wave model:

   B. E. Treeby, J. Jaros, D. Rohrbach, B. T. Cox , "Modelling elastic wave 
   propagation using the k-Wave MATLAB toolbox," IEEE International 
   Ultrasonics Symposium, pp. 146-149, 2014.
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