3_Installation.txt

/**

\page Installation Installation Guidelines

The following steps describe the whole procedure to build and install CBICATk. 

# 1. Dependencies

Before building the CBICA Toolkit (CBICATk), the following software libraries are required to be installed. <strong>Please note</strong> that to build in Windows, CMake needs to be used an appropriate compiler (Win32 or Win64 version of Visual Studio is recommended). The selected solution platform is needed to match with dependent libraries.

<table border="0">
	<tr>
    <td width="10%"><strong>Package</strong></td>      
	  <td width="10%"><strong>Version</strong></td>      
    <td width="80%"><strong>Description</strong></td>  
	</tr>
	<tr>
		<td>Archiver</td>
		<td></td>
		<td>(<a href="http://www.7-zip.org/">7-zip</a> for Windows, gzip for Linux)</td>
	</tr>
	<tr>
		<td>C++ compiler</td>
		<td></td>
		<td>(MSVC/11.x, MSVC/12.x, GCC/4.8.1, GCC/4.9.2)</td>
	</tr>
	<tr>
		<td><a href="http://www.cmake.org/">CMake</a></td>
		<td>2.8.4 or higher</td>
		<td>To compile and build CBICATk and its dependencies</td>
	</tr>
	<tr>
		<td><a href="http://www.itk.org/ITK/resources/software.html">ITK</a></td>
		<td>4.7 or higher</td>
		<td>Build VTK before proceeding to compile ITK. Instructions to compile ITK are given <a href="http://www.itk.org/Wiki/ITK/Configuring_and_Building">here</a>. During CMake configuration, enable the <b>Module_ITKVtkGlue</b> flag</td>
	</tr>
	<tr>
		<td><a href="opencv.org/downloads.html">OpenCV</a></td>
		<td>3.0 or higher</td>
		<td>All machine learning algorithms. This generally comes pre-compiled; if not found for your system, steps similar to those done for VTK and ITK can be done.</td>
	</tr>
	<tr>
		<td><a href="http://www.stack.nl/~dimitri/doxygen/">Doxygen</a></td>
		<td></td>
		<td>[OPTIONAL] For documentation only</td>
	</tr>
</table>

Ensure all dependencies are met before proceeding. 

# 2. Build

Please follow commands below in a shell/terminal (e.g., <a href="http://www.gnu.org/software/bash/">Bash</a>). They will configure and build CBICATk using <a href="http://www.gnu.org/software/make/">GNU Make</a>. The main CMake configuration file (CMakeLists.txt) is located in the root directory of the package.

## 2.1 Extract source files and create the build directory

\verbatim
tar xzf CBICATk-${version}-source.tar.gz
mkdir CBICATk-${version}-build
cd CBICATk-${version}-build
\endverbatim
[Note: In Windows, an appropriate compression program (e.g., <a href="http://www.7-zip.org/">7-zip</a>) might be used to extract the files.]

## 2.2  Run CMake to configure the build tree

\verbatim
cmake ../CBICATk-${version}-source
\endverbatim
Use the CMake variable CMAKE_INSTALL_PREFIX to specify the installation
directory, as in:
\verbatim
cmake -DCMAKE_INSTALL_PREFIX=/opt/software/geodesic ../CBICATk-${version}-source
\endverbatim

For <b>Windows</b>, open CMake-GUI and select <code>CBICATk-${version}-source</code> as the "source" directory and select <code>CBICATk-${version}-build</code> as the "build" directory. Click on "Configure" and select the appropriate C++ compiler. If there weren't any configuration errors, click "Generate".

CMake should be able to find the dependencies if they are specified in the <code>$PATH</code> variable in your environment. If you have custom installation directories, then ensure that they have been added to the <code>$PATH</code> variable or point the variable(s) <b>${Dependency}_DIR</b> to the appropriate build paths where <code>${Dependency}Config.cmake</code> is/are present (for example, in the case of ITK, point <code>ITK_DIR</code> to the directory where <code>ITKConfig.cmake</code> is present) - this should be either the build directory or the installation directory. If you are using a bash shell, it can be done using the following command:

\verbatim
cmake -DITKDIR=${path_to_custom_ITK_build_dir} -DOpenCV_DIR=${path_to_custom_OpenCV_build_dir} CBICATk-${version}-source
\endverbatim

This step will generate platform-specific project files (for example, Make file for GCC and Visual Studio solution file for MSVC).

Some of the options that can be set are:

<table border="0">
	<tr>
		<td>BUILD_DOCUMENTATION</td>
		<td>Builds the documentation from scratch</td>
	</tr>
	<tr>
		<td>BUILD_TESTING</td>
		<td>Enables unit testing</td>
	</tr>
	<tr>
		<td>CMAKE_INSTALL_PREFIX</td>
		<td>Path where the project will be installed</td>
	</tr>
</table>

## 2.3 Compile the project

\verbatim
make
\endverbatim

For <b>Windows</b>, you should launch the generated solution file of Visual Studio (by default, only <code>Release</code> version of the code will be compiled - if this needs to be changed, it can be done so by editing the variable <code>CMAKE_CONFIGURATION_TYPE</code> during the CMake configuration step), and then build solution.

## 2.3 [OPTIONAL] Compile the documentation

To build the documentation from scratch, the <code>BUILD_DOCUMENTATION</code> option in the CMake configuration needs to be enabled.

\verbatim
make doc
\endverbatim

For <b>Windows</b>, build the <b>doc</b> project in the loaded solution.

## 2.4 [OPTIONAL] Test 

To perform tests, the <code>BUILD_TESTING</code> option in the CMake configuration needs to be enabled.

\verbatim
make test
\endverbatim

For <b>Windows</b>, you should build the <b>RUN_TESTS</b> project.

In case of failing tests, re-run the tests, but this time by executing <a href="http://www.cmake.org/cmake/help/v2.8.8/ctest.html">CTest</a> directly with the '-V' option to enable verbose output and redirect the output to a text file, as in the example below (works for both Windows and Linux on the command line or shell):

\verbatim
ctest -V >& CBICATk-test.log
\endverbatim

And send the file <b>CBICATk-test.log</b> as attachment of the issue report to <mailto:software@cbica.upenn.edu>.

## 2.4 [OPTIONAL] Install 

\verbatim
make install
\endverbatim

For <b>Windows</b>, you should build the <b>INSTALL</b> project.

Upon the success of the above compilation and build process, CBICATk is installed into the directory specified by the <code>CMAKE_INSTALL_PREFIX</code>, which was set during step 2.2 above.

*/