k-Wave

1. styxed
   

   Member
   Joined: Oct '12
   Posts: 6

   Hi,

   I don't have Matlab and have been doing k-Wave simulations with Octave without any problems. Now I need to create the HDF5 file for running C++ but Octave only seems to support HDF5 via the save command: http://www.gnu.org/software/octave/doc/interpreter/Simple-File-I_002fO.html
   Is it possible to change the code in writeMatrix.m in such a way that I can make the HDF5 file with the save command and the -hdf5 option? I am asking because I don't seem to be able to set the attributes of the matrices nor the holder properties manually with the save command.

   Thanks for your help.

   Erik

   Posted 10 years ago #

2. Bradley Treeby
   

   Developer
   Joined: Mar '10
   Posts: 1,640

   Hi Erik,

   The HDF5 files needed for the C++ code are required to be in a specific format, with particular field names and attributes for each variable (the specifics are detailed in the k-Wave manual). Unfortunately, I don't think using the save command in Octave will allow you this flexibility as it doesn't give you access to the different high-level functions in the HDF5 library.

   If you are comfortable programming in C/C++, one possibility would be to write a mex file that takes your data from MATLAB and writes it to disk using the HDF5 API.

   Brad.

   Posted 10 years ago #

3. jbishop
   

   Member
   Joined: Oct '18
   Posts: 5

   There is now a package hdf5oct available from github that provides the necessary hdf5 read/write functions for octave. There were a few steps to get it to work:

   I have octave 4.4.1 and hdf5 1.10.4 installed. I installed the hdf5 from source, so I specified the location explicitly for building octave ./configure --with-hdf5-libdir='/usr/local/hdf5/lib' --with-hdf5-includedir='/usr/local/hdf5/include'

   The reason the latest octave 4.4.1 was needed is it has support for handle classes, which the octave version available by dpkg/apt-get may or may not.

   hdf5oct had a couple of slight problems. The github code from 4 years ago somehow does not pick up the HDF libraries. There is a modified version of the h5read.cc source here:

   https://raw.githubusercontent.com/tmullins/hdf5oct/2c4b1c412f67cc8b11923054756e001c4161db39/h5read.cc

   which is fixed for this problem. Then a second issue at line 979 of that modified h5read.cc, i edited:
   979 int rank = ov_data.dims ().numel ();
   to become:
   979 int rank = ov_data.ndims ();

   after that there was only one other edit, at getComputerInfo.m line 54 system_dependent is a matlab command, replace with uname or computer in octave, it is only a text field so anything will do.

   At this point the c++ binaries are running in the example_us_beam_patterns.

   Posted 5 years ago #

4. jbishop
   

   Member
   Joined: Oct '18
   Posts: 5

   Forgot to mention, but with the local install of hdf5, had to add this to the hdf5oct makefile as well:

   -I/usr/local/hdf5/include -L/usr/local/hdf5/lib -L/usr/local/hdf5/lib/libhdf5.a

   and there was a message about -fPIC flag so I added that too.

   Posted 5 years ago #

5. Jiri Jaros
   

   Developer
   Joined: Feb '12
   Posts: 115

   Thanks jbishop for sorting this out.

   One thing to mention here. HDF5 versions 1.8.x and 1.10.x are not compatible (has a different data layout under some circumstances). In the actual version of k-Wave, we do not use any features from HDF5 1.10.x, thus it should be possible to read files created with HDF 1.10.x using 1.8.x. However, this may change in the future. The reason I mention it is that Matlab only supports HDF5 1.8.x.

   Best,
   Jiri

   Posted 5 years ago #

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