k-wave-toolbox-version-1.1
所属分类:matlab编程
开发工具:matlab
文件大小:4019KB
下载次数:94
上传日期:2014-10-21 19:35:07
上 传 者:
wangcongzhi
说明: 采用k空间方法仿真超声声场及光声、剪切波传播等的专用matlab工具箱程序包,能模拟非均匀介质情况下的波动传播情况,功能强大,
(k-wave toolbox for ultrasound simulation)
文件列表:
k-Wave (0, 2014-10-02)
k-Wave\Contents.m (8323, 2014-10-02)
k-Wave\addNoise.m (2787, 2014-10-02)
k-Wave\applyFilter.m (7861, 2014-10-02)
k-Wave\attenComp.m (21639, 2014-10-02)
k-Wave\attenuationWater.m (2349, 2014-10-02)
k-Wave\beamPlot.m (3890, 2014-10-02)
k-Wave\benchmark.m (8306, 2014-10-02)
k-Wave\binaries (0, 2014-10-02)
k-Wave\cart2grid.m (6879, 2014-10-02)
k-Wave\checkFactors.m (2594, 2014-10-02)
k-Wave\checkStability.m (6000, 2014-10-02)
k-Wave\db2neper.m (1578, 2014-10-02)
k-Wave\envelopeDetection.m (2404, 2014-10-02)
k-Wave\examples (0, 2014-10-02)
k-Wave\examples\EXAMPLE_k-Wave.png (5291, 2014-10-02)
k-Wave\examples\EXAMPLE_shepp_logan.mat (19845, 2014-10-02)
k-Wave\examples\EXAMPLE_source_one.png (332, 2014-10-02)
k-Wave\examples\EXAMPLE_source_two.bmp (32830, 2014-10-02)
k-Wave\examples\example_cpp_io_in_parts.m (12173, 2014-10-02)
k-Wave\examples\example_cpp_running_simulations.m (7539, 2014-10-02)
k-Wave\examples\example_ewp_3D_simulation.m (4220, 2014-10-02)
k-Wave\examples\example_ewp_layered_medium.m (4128, 2014-10-02)
k-Wave\examples\example_ewp_plane_wave_absorption.m (6885, 2014-10-02)
k-Wave\examples\example_ewp_shear_wave_snells_law.m (6460, 2014-10-02)
k-Wave\examples\example_ivp_1D_simulation.m (3038, 2014-10-02)
k-Wave\examples\example_ivp_3D_simulation.m (3768, 2014-10-02)
k-Wave\examples\example_ivp_binary_sensor_mask.m (3691, 2014-10-02)
k-Wave\examples\example_ivp_comparison_modelling_functions.m (4737, 2014-10-02)
k-Wave\examples\example_ivp_heterogeneous_medium.m (3315, 2014-10-02)
k-Wave\examples\example_ivp_homogeneous_medium.m (3232, 2014-10-02)
k-Wave\examples\example_ivp_loading_external_image.m (3043, 2014-10-02)
k-Wave\examples\example_ivp_opposing_corners_sensor_mask.m (3945, 2014-10-02)
k-Wave\examples\example_ivp_photoacoustic_waveforms.m (4892, 2014-10-02)
k-Wave\examples\example_ivp_recording_particle_velocity.m (4047, 2014-10-02)
k-Wave\examples\example_ivp_saving_movie_files.m (2972, 2014-10-02)
k-Wave\examples\example_ivp_sensor_frequency_response.m (4043, 2014-10-02)
k-Wave\examples\example_ivp_setting_initial_gradient.m (3616, 2014-10-02)
k-Wave\examples\example_na_controlling_the_PML.m (4070, 2014-10-02)
k-Wave\examples\example_na_filtering_part_1.m (3574, 2014-10-02)
... ...
____________________________________________________________________________
k-Wave
A MATLAB toolbox for the time-domain
simulation of acoustic wave fields
____________________________________________________________________________
VERSION INFORMATION
____________________________________________________________________________
Version 1.1, Released 3rd October 2014
Written by Bradley Treeby, Ben Cox, and Jiri Jaros
Tested using:
Mac OS X Lion: MATLAB R2011a, R2014a
Windows 7 ***-bit: MATLAB R2008a through to R2014a
Linux Ubuntu 12.04, 14.04: R2013a, R2014a
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.
____________________________________________________________________________
PRODUCT OVERVIEW
____________________________________________________________________________
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.
____________________________________________________________________________
INSTALLATION INSTRUCTIONS
____________________________________________________________________________
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 dropdown menus (File -> Set Path) if using
MATLAB 2012a and earlier, or the the "Set Path" button on the ribbon bar if
using MATLAB 2012b and later. 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. In versions of MATLAB
prior to 2012b, the help browser is opened by clicking on the blue question
mark icon on the menu bar. In MATLAB 2012b (and later), the documentation is
accessed by selecting "Help" from the ribbon bar, and then clicking on
"Supplemental Software". 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.
____________________________________________________________________________
RELEASE NOTES
____________________________________________________________________________
New Features and Changes:
- simulations in elastic media are now supported using the pstdElastic2D and
pstdElastic3D functions
- 3D simulations can be run on an NVIDIA graphics processing unit (GPU)
using a native C++/CUDA code
- rectangular binary sensor masks can be defined by assigning the grid
coordinates of two opposing corners to sensor.mask
- sensor.record now supports the additional input options 'p_min',
'p_max_all', 'p_min_all', 'u_min', 'u_max_all', 'u_min_all', and
'u_non_staggered'
- simulation functions have been restructured to reduce code duplication
- the accuracy of the acoustic intensity output for frequencies close to
Nyquist limit has been improved
- the C++ code now supports command line inputs for checkpoint-restart and
importing FFTW wisdom
- the C++ code now exploits AVX instructions in addition to SSE
- attenuation compensation for photoacoustic tomography can be performed
using time-variant filtering via attenComp
- vessel filtering for photoacoustic tomography can be performed using
vesselFilter
- kspaceFirstOrder3DC now supports optional inputs to specify the name and
location of the binary and data files
- makeSphere and makeSphericalSection can be set to return logical matrices
to reduce memory usage
- resize now supports 1D inputs
- checkFactors now also reports prime numbers
Bug Fixes:
- bug fix in using a Cartesian sensor mask with nearest neighbour
interpolation and sensor.record set to 'p_min' (generated error)
- bug fix in using sensor.directivity_angle with the optional input 'DataCast'
set to 'gpuArray-single' (generated error)
- bug fix in kspaceFirstOrder3DC when performing time reversal image
reconstruction using sensor.time_reversal_boundary_data with 'PMLInside' set
to false (PML was not removed)
- bug fix in kspaceFirstOrder3DC when calling script on a different drive
using Windows (generated error)
- bug fix in kspaceSecondOrder when setting absorption values with
medium.alpha_power to values less than 1 (returned NaN)
- bug fix in kspaceSecondOrder when using sensor.record = {'p_final'}
(generated error, grid expansion not removed)
- bug fix in makeSphere for grid sizes with uneven dimensions (generated
error)
- bug fix in makeSphere to centre sphere on the kgrid origin (previously
offset by 1)
- bug fix in writeMatrix for source variables larger than 1 MB (incorrect
chunk size generated error)
New Functions:
- attenComp
- checkStability
- fitPowerLawParams
- getBLI
- getSpacedPoints
- h5compare
- kspaceFirstOrder3DG
- maxND
- minND
- overlayPlot
- pstdElastic2D
- pstdElastic3D
- revolve2D
- timeShift
- vesselFilter
- writeAttributes
- writeFlags
- writeGrid
New Examples:
- Defining A Sensor Mask By Opposing Corners
- Attenuation Compensation Using Time Variant Filtering
- Running C++ Simulations
- Saving Input Files in Parts
- Explosive Source In A Layered Medium
- Plane Wave Absorption
- Shear Waves And Critical Angle Reflection
- Simulations In Three Dimensions
____________________________________________________________________________
LICENSE
____________________________________________________________________________
k-Wave (c) 2009-2014 Bradley Treeby and Ben Cox
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:
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.
and/or
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.
along with any other relevant publications. The first paper gives an
overview of the toolbox with applications in photoacoustics, and the second
describes the nonlinear ultrasound model and the C++ code.
____________________________________________________________________________
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