===== Set up ROS =====

Recommended operating system is Ubuntu 12.04 LTS 64bit.

Install ROS Groovy (see ''http://www.ros.org/wiki/groovy/Installation/Ubuntu''):

  sudo apt-get install ros-groovy-desktop-full
  

====== Installing RoboSherlock ======

Last Update: May 15th, 2013

Tested on: Ubuntu 12.04 with ROS Groovy

==== Standard libraries and PCL ====

First of all install some standard libraries and PCL trunk

  sudo apt-get install libicu-dev libxerces-c-dev openjdk-7-jdk libapr1-dev ros-groovy-pcl ros-groovy-openni-camera ros-groovy-openni-launch
  
For using pcl trunk with groovy see:
  http://answers.ros.org/question/62979/how-do-i-use-pcl-17-with-groovy/
  
**Note:** you need to enable the //RSD// feature from the features submodule in pcl. To do this go to pcl root directory cd to features and edit the //CMakeLists.txt// file. Uncomment the lines contatining //rsd.h// //rsd.cpp// and //rsd.hpp//. Remake the project (don't do clean!!!!)
==== Installation location ====

Choose an installation location

  cd $HOME
  mkdir uima

==== Set up Bash ====

Put the right paths into your ~/.bashrc. In the following code, replace ''$HOME/uima'' with the location where you actually want your UIMA environment to reside.

  export UIMA_WORKSPACE=$HOME/uima
  export UIMA_HOME=$UIMA_WORKSPACE/apache-uima
  export UIMACPP_HOME=$UIMA_WORKSPACE/uimacpp/install
  
  export PATH=$UIMACPP_HOME/bin:$UIMA_WORKSPACE/apache-uima/bin:$PATH
  export LD_LIBRARY_PATH=$UIMACPP_HOME/lib:$UIMA_WORKSPACE/iai-uima/ias-uima-cpp/lib:$LD_LIBRARY_PATH
  export CLASSPATH=$UIMA_WORKSPACE/iai-uima/ias_uima_rosjava/build/classes/main
  
  export APR_HOME=/usr
  export ICU_HOME=/usr
  export XERCES_HOME=/usr  
    
  export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64/ 
  export JAVA_INCLUDE=$JAVA_HOME/include

==== UIMA/C++ ====
Get UIMA/C++ from the SVN & build

  cd $UIMA_WORKSPACE
  svn co https://svn.apache.org/repos/asf/uima/uimacpp/trunk/ uimacpp

uimacpp will look for libapr-1.0.so which isn't there in Ubuntu, so we need to create a symlink to that:

  cd /usr/lib
  sudo ln -s libapr-1.so libapr-1.0.so

Note: recent trunk seems to have a different build system setup, I had to do:

  cd $UIMA_WORKSPACE/uimacpp
  ./autogen.sh
  ./configure --without-activemq --with-jdk=/usr/lib/jvm/java-7-openjdk-amd64/include --prefix=${UIMACPP_HOME}
  make install

What this will do is compile everything and create a couple of folders in ''$UIMACPP_HOME'', so ''ls $UIMACPP_HOME'' should give you:
  
  bin  data  include  lib


==== UIMA Java SDK ====
Get the UIMA Java SDK Binaries. Download and extract latest binaries to ''$UIMA_WORKSPACE''

  http://uima.apache.org/downloads.cgi

Doing ''ls $UIMA_WORKSPACE/apache-uima'' should give something like

  bin  config  docs  eclipsePlugins  examples  issuesFixed  lib  LICENSE  NOTICE  README  RELEASE_NOTES.html

==== Set up MongoDB ====

(Might not be needed)
Get the server (vs. 2.4.5 64bit). See: 
[[http://www.mongodb.org/downloads]]

Get the client (vs. 2.2-latest) and unpack it to $UIMA_WORKSPACE
[[http://dl.mongodb.org/dl/cxx-driver/]] 

If you don't yet have it, get scons

  sudo apt-get install scons
  
Before compiling the client, uncomment the following line in src/SConscript.client
  
  env.SharedLibrary('mongoclient', clientSource),
  
Add the env variables for mongo to your ''.bashrc''. Remember to source your newly edited bashrc file.
  
  export MONGODBCLIENT_HOME=$UIMA_WORKSPACE/mongo-cxx-driver-v2.2/
  export MONGODBCLIENT_HOME_INCLUDE=$MONGODBCLIENT_HOME/src
  export LD_LIBRARY_PATH=$MONGODBCLIENT_HOME:$LD_LIBRARY_PATH

Now ''cd'' to ''MONGODBCLIENT_HOME'', call ''scons''
==== The IAS UIMA Repository ====
Get the IAS UIMA Repository. Check out code and submodules:

  cd $UIMA_WORKSPACE
  git clone git@github.com:code-iai/iai-uima.git
  cd iai-uima
  git submodule init
  git submodule update

Checkout dependencies and add them to your ROS_PACKAGE_PATH:

  git clone git@github.com:code-iai/iai_perception.git
  git clone git@github.com:code-iai/entres.git
  git clone git@github.com:code-iai/iai_common_msgs.git
  git clone git@github.com:code-iai/designator_integration.git
 
Setup rosjava
  
Check out rosjava_core to your catkin ws:
  git clone git@github.com:rosjava/rosjava_core.git -b groovy-devel
Details on how to make the project are here:
  http://docs.rosjava.googlecode.com/hg/rosjava_core/html/index.html


Now call

  catkin_make

**Note:** for single core machines run with //-j2//

Now ''ls $UIMA_WORKSPACE/iai-uima/ias_uima_rosjava/build/classes/main/org/uima/collectionreader'' should show:

  Clock.class
  
To install apache, php and other things required for the database visualization website, look at ''$UIMA_WORKSPACE/iai-uima/www/README.txt''. To get histograms visualized as graphs, install //libphp-jpgraph//.
===== Run Example =====
  roslaunch openni_launch openni.launch
  rosrun rqt_reconfigure rqt_reconfigure # enable depth registration and hiRes RGB
  cpeGui.sh # use as collection reader ias-uima-java/desc/ClockDescriptor and as analysis engine ias-uima-cpp/descriptors/analysis_engines/iaiGoggles.xml
  
  
===== Troubleshooting =====

In case the website complains that sorting needs mongodb index do the following...
  
  mongo uima
  db.uima.ensureIndex({"scenes.timestamp":-1})
  //double check : 
  db.uima.getIndexes()
 
In case your RosKinnectBridge hangs check if depth registered is turned on in openni. You can do this by listening to the topic:

  rostopic hz /camera/depth_registered/points
  
If RosKinectBridge fails check the parameters for tf ''from'', ''to'' and ''camera frames'' in the description of the annotation. 

===== Known Issues =====

FeatureClassifierAnnotator does not work if you link it to //plc_io or pcl_visualizer//. This is due to the incompatibility of the native //hdf5// library that comes with Ubuntu and the one used by the //icf// package