http://www.k-wave.org/forum/topic/creating-hdf5-input-files-in-octave Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:28:24 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/creating-hdf5-input-files-in-octave#post-6657 Wed, 21 Nov 2018 14:44:35 +0000 Jiri Jaros 6657@http://www.k-wave.org/forum/ <p>Thanks jbishop for sorting this out.</p> <p>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.</p> <p>Best,<br /> Jiri </p> http://www.k-wave.org/forum/topic/creating-hdf5-input-files-in-octave#post-6655 Sat, 17 Nov 2018 18:57:04 +0000 jbishop 6655@http://www.k-wave.org/forum/ <p>Forgot to mention, but with the local install of hdf5, had to add this to the hdf5oct makefile as well:</p> <p>-I/usr/local/hdf5/include -L/usr/local/hdf5/lib -L/usr/local/hdf5/lib/libhdf5.a</p> <p>and there was a message about -fPIC flag so I added that too. </p> http://www.k-wave.org/forum/topic/creating-hdf5-input-files-in-octave#post-6654 Sat, 17 Nov 2018 13:41:35 +0000 jbishop 6654@http://www.k-wave.org/forum/ <p>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:</p> <p>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'</p> <p>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.</p> <p>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:</p> <p><a href="https://raw.githubusercontent.com/tmullins/hdf5oct/2c4b1c412f67cc8b11923054756e001c4161db39/h5read.cc" rel="nofollow">https://raw.githubusercontent.com/tmullins/hdf5oct/2c4b1c412f67cc8b11923054756e001c4161db39/h5read.cc</a></p> <p>which is fixed for this problem. Then a second issue at line 979 of that modified h5read.cc, i edited:<br /> 979 int rank = ov_data.dims ().numel ();<br /> to become:<br /> 979 int rank = ov_data.ndims (); </p> <p>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. </p> <p>At this point the c++ binaries are running in the example_us_beam_patterns. </p> http://www.k-wave.org/forum/topic/creating-hdf5-input-files-in-octave#post-3910 Tue, 03 Sep 2013 19:26:52 +0000 Bradley Treeby 3910@http://www.k-wave.org/forum/ <p>Hi Erik,</p> <p>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.</p> <p>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.</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/creating-hdf5-input-files-in-octave#post-3909 Tue, 03 Sep 2013 15:25:58 +0000 styxed 3909@http://www.k-wave.org/forum/ <p>Hi,</p> <p>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 <code>save</code> command: <a href="http://www.gnu.org/software/octave/doc/interpreter/Simple-File-I_002fO.html" rel="nofollow">http://www.gnu.org/software/octave/doc/interpreter/Simple-File-I_002fO.html</a><br /> Is it possible to change the code in <code>writeMatrix.m</code> in such a way that I can make the HDF5 file with the <code>save</code> command and the <code>-hdf5</code> 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 <code>save</code> command.</p> <p>Thanks for your help.</p> <p>Erik </p>