Link to project website: https://mrsdprojects.ri.cmu.edu/2020teama/

1. Install ROS (please use ros-kinetic)
2. Install dVRK simulation evironments

$ sudo apt-get install libxml2-dev libraw1394-dev libncurses5-dev qtcreator swig flite sox espeak cmake-curses-gui cmake-qt-gui libopencv-dev git subversion gfortran libcppunit-dev
$ sudo apt-get install qt5-default
$ sudo apt-get install python-catkin-tools
$ source /opt/ros/kinetic/setup.bash
$ mkdir -p ~/catkin_ws/src  
  #Change [catkin_ws] to whatever name you want
$ cd ~/catkin_ws/
$ catkin init #This creates a hidden .catkin_tools directory in the specified workspace.
$ cd ~/catkin_ws/src
$ git clone https://github.com/jhu-cisst/cisst-saw --recursive
$ cd ~/catkin_ws
$ catkin config --cmake-args -DCMAKE_BUILD_TYPE=Release 
  # At this point you might see there things that are still missing from the package "build", "devel". These things would be built in the next step.
$ catkin build #This might take a while
$ source devel/setup.bash
$ cd ~/catkin_ws/src
$ git clone https://github.com/jhu-dvrk/dvrk-ros
$ git clone https://github.com/jhu-dvrk/dvrk-gravity-compensation
$ cd ~/catkin_ws
$ catkin build
$ cd src 
$ git clone https://github.com/biorobotics/Medical-DVRK-AR.git
$ cd ~/catkin_ws
$ catkin build

3. install open3d version 0.7.0

your_workspace/
  build/
  devel/
  logs/
  src/
    cisst-saw/
    dvrk-gravity-compensation/
    dvrk-ros/
    Medical-DVRK-AR/
      config/
      data/
      launch/
      src/
      srv/
       :
      [blablablabla]
       :

First terminal:

$ roscore 

Second terminal:

$ source ~/your_workspace/devel/setup.bash
$ roslaunch medical_dvrk_ar dvrk_arm_rviz.launch arm:=PSM1

Press Power-On, then Home

Third terminal:

$ rosrun medical_dvrk_ar blaser_sim.py -j ~/your_workspace/src/Medical-DVRK-AR/config/blaser_SIMULATED.json

In Rviz: After launching Rviz, add in the following two rostopics to visualize the results 1)pointcloud2 2)makerarray.

1. Add the .stl file in the "data/" folder.
2. Edit "/config/blaser_SIMULATED.json" line:47(mesh_resource) to the new .stl file path.
3. Run blaser_sim.py .

1. Run "python Modeling/pc_sticher.py" to start listener.
2. Add the "Pointcloud2" topic by the name "organ_3d_point_cloud".
3. Run any robot control script under the dvrkPlanner folder.

1. cd /your_file_path/src/Medical-DVRK-AR/src/medical_dvrk_ar/Modeling/
2. python3 visualize_points_norm.py --path '../../../data/60degree_norm.npy'
3. you can change '60degree_norm.npy' to '80degree_norm.npy' which contain more norm vectors
4. In Rviz choose ADD > ADD by topic > the pose array msg
5. In Rviz choose ADD > ADD by topic > the point cloud2 msg

1. cd /your_file_path/src/Medical-DVRK-AR/src/medical_dvrk_ar/Modeling/
2. python stiffness_map.py --path /path-to-local-repo/Medical-DVRK-AR/data/xyz_for_stiffness_est.npy --map_type b
3. If you want a strictly binary stiffness map, it is "--map b". If you want create a normalized heat map, it is "--map h".
4. The liver with tumors (red) should pop up in matplotlib
5. check the genetrated file "points_with_stiffness.npy" in /Medical-DVRK-AR/data folder
6. cd /your_file_path/src/Medical-DVRK-AR/src/medical_dvrk_ar/Modeling/
7. python3 visualize_stiffness.py --path /path-to-local-repo/Medical-DVRK-AR/data/points_with_stiffness.npy
8. In Rviz, add Pointcloud2 in liverStiffness topic, you should see a "grey blue" liver
9. Change the "size" to 0.0005, you should see the "red" tumor

Please first install scikit-learn==0.20 (Previous version may not have the module we need)

1. run roscore
2. launch dvrk psm arm with command mentioned above
3. run blaser_sim.py with command mentioned above
4. The gaussian process palpation is in the dvrkPlanner fold

$ python gp.py --path ~/your_workspace/src/Medical-DVRK-AR/data/palpation_path_25rows_25cols.npy --dest ~/your_workspace/src/Medical-DVRK-AR/src/medical_dvrk_ar/dvrkPlanner/