Editing Archive (section)

=Bone lab libraries=
A library of reusable bits for the kinds of things we do in the lab. Built on VTK and ITK and other toolkits.

==Overview==

The main libraries are vtkski and itkski.  These provide various VTK and ITK classes respectively that can be used in other programs.

Refer to
* [[vtkski development]]
* [[itkski development]]

See [[Bone lab applications]] for Applications that make use of these libraries

You may want to consider using vtkn88 from the Numerics88 software.  vtkn88 is not as extensive as vtkski, but it is better maintained and better tested.
See [http://mike.kin.ucalgary.ca/numerics88/manual/html/#vtkn88 the section on vtkn88] in the Numerics88 manual.

To make things more confusing, quite a bit of old code is actually in vtkMy (see [[vtkMy development]]).  It will be ported eventually to vtkski or itkski.  Generally if you need to use something there, it is better to port the specific parts you need to vtkski or itkski or Applications.

==Build Instructions==

===Prerequisites===

Refer the to development page corresponding to your system:
* [[Development on OS-X]]
* [[Development on Windows]]
* [[Development on Linux]]

You should find there lists of required software, as well as installation instructions. 

===Getting the source code===

Choose a place in your home directory that you want to use for the source code.  For example

 mkdir -p ~/code/bonelab
 cd ~/code/bonelab

(Note that '~' gets automatically expanded to your home directory.)

Get the sources from the subversion repository.

 svn checkout https://mike.kin.ucalgary.ca/svn/bonelab/trunk

See the section on svn for more info: [[Subversion (SVN)]] .

===Compiling===

====Create a build directory====

Create a build directory in trunk/Libraries and use cmake to configure the build:

 cd trunk/Libraries
 mkdir build
 cd build

====setenv.sh====

If you're using setenv.sh scripts (see [[Development_on_OS-X#Scripts to Set Environment Variables]]), here is a template.  You'll have to adjust the paths for your system.  Put this is the build directory; source it before configuring with cmake, and cmake should find everything itself.

<source lang=bash>
#!/bin/bash
#
# setenv.sh for bonelab Libraries.
 
source /opt/boost-1.49.0/setenv.sh
source /opt/itk-3.20.1/setenv.sh
source /opt/vtk-5.10.0/setenv.sh
 
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

export BONELAB_LIBRARIES_DIR="${SCRIPT_DIR}/bin"
export vtkski_DIR="${SCRIPT_DIR}/vtkski"

remove_path DYLD_LIBRARY_PATH '/opt/bonelab(-[^/]+)?/lib/?'
remove_path DYLD_LIBRARY_PATH '.*/bonelab/.*/Libraries/.*'
add_path DYLD_LIBRARY_PATH "${BONELAB_LIBRARIES_DIR}"
remove_path PYTHONPATH '/opt/bonelab(-[^/]+)?/lib/?'
remove_path PYTHONPATH '.*/bonelab/.*/Libraries/.*'
add_path PYTHONPATH "${BONELAB_LIBRARIES_DIR}"
</source>

Of course, the exact paths will depends on the versions and where you installed them.  This is an optional step, but it does make configuring cmake easier.

It also makes accessing the libraries easier from other software.

=====configuring with cmake=====

So now for configuring cmake:

 cmake-gui ..

Here are some typical configuration options:

{| border="1" cellpadding="2" cellspacing="0"
|-
! option
! Setting
! Comments
|- valign="top"
| CMAKE_BUILD_TYPE || Release || If not set, that's fine, but you'll get more optimized (i.e. faster) binaries if you set this to Release.
|- valign="top"
| CMAKE_INSTALL_PREFIX || /opt/bonelab-r2970 || You don't actually have to set anything for this, as bonelab can be run from the build directory.  However, if you do install it, it's probably best to include the specific SVN revision number in the directory name.
|- valign="top"
| VTK_DIR || /opt/vtk-5.10.0/lib/vtk-5.10  || Set this to wherever you installed VTK.  If you intend to build the paraview extensions as plugins, then you set this to the internal version of VTK inside the paraview build directory.  (See [[Paraview development]] if you need to install ParaView).
|- valign="top"
| BONELAB_BUILD_LIBRARY_itkski  || ON/OFF || Set this to OFF if you don't want to build itkski as well.  In this case you won't need to have ITK installed or specify where it can be found.
|- valign="top"
| ITK_DIR || /opt/itk-3.20.1/lib/InsightToolkit || You only need to set this if BONELAB_BUILD_LIBRARY_itkski is ON.  In that case, set it to wherever you installed ITK.
|- valign="top"
| Boost_INCLUDE_DIR  ||  /opt/boost-1.47.0/include || Set this to wherever you installed boost.  Note that this is an Advanced setting, and you won't see it until you toggle to Advanced view.  Don't worry about all the Boost libraries it doesn't find; as soon as Boost_INCLUDE_DIR is properly set, it will find them.
|- valign="top"
| PYTHON_INCLUDE_DIR || /Library/Frameworks/Python.framework/Versions/2.7/Headers || This is if you've installed a more recent version on OS-X than the default version included in OS-X.  CMake tends to always find the default version.
|- valign="top"
| PYTHON_LIBRARY || /Library/Frameworks/Python.framework/Versions/lib/libpython2.7.dylib || See the comments for PYTHON_INCLUDE_DIR
|}

Once you're happy with your settings, hit Configure.  You might have to hit it a couple of times until there are no more errors, and the Generate button is enabled.  Then hit Generate and quite cmake-gui.

Now run:

 make

You won't usually need to run a 'make install', since you can just use vtkski from your build directory.

===Building Doxygen documentation===

This is an advanced topic.  Most users can just refer to the documentation here: http://mike.kin.ucalgary.ca/vtkski/ .

To build the Doxygen documentation, set the cmake variable BUILD_DOCUMENTATION to ON.  This variable is marked as advanced.  You will need to have installed Doxygen ( http://www.doxygen.org/ ) in order to build the documentation.

The documentation is not automatically built with make (it takes a very long time to build).  Instead, you will need to explicitly request it, like this:
 make  vtkskiDoxygenDoc

Warning: You must build against a source code tree of VTK, rather than a binary install.  This is because certain scripts from the VTK source code directory are required to build the documentation.  (Explicitly, the cmake variable VTK_DIR should be something like /Users/eric/source/vtk-5.6.0/build and not something like /opt/vtk-5.6.0/lib/vtk-5.6 ).

===Installing===

For personal use, just use the bonelab libraries from the build directories.  However, for making available to everyone on the system, you can do this:

 sudo make install

This should be done for both the Libraries and the Applications (run from the respective build directories).  It will install a setenv.sh script, but it's usually a good idea to fix it up so the paths for vtk and itk are also set.  Typically add lines like this near the beginning of the setenv.sh file in the installation directory:

 source /opt/vtk-5.10.0/setenv.sh
 source /opt/itk-3.20.1/setenv.sh

These should match exactly the versions that were used to build bonelab.

==Building the Applications==

Similar process to building the libraries, except that you create the build directory in Applications/build , and do everything from there.

====Installing the Doxygen documentation on mike.kin====

I recommend that you build the documentation with the cmake flag DOCUMENTATION_HTML_TARZ set to on (this variable is an advanced setting).  Then the build process will automatically make a tar ball of all the HTML documentation, build/Utilities/Doxygen/vtkski-html.tar.gz , which is easy to copy over to mik.kin (using FTP or scp or the mounted Data0 volume).

The documentation needs to live in /Library/WebServer/Documents/vtkski .  The commands would look something like this
 tar xvzf vtkski-html.tar.gz
 sudo rm -rf /Library/WebServer/Documents/vtkski     # remove old docs
 sudo mv html /Library/WebServer/Documents/vtkski
 sudo chown -R root /Library/WebServer/Documents/vtkski