continuous_palpation

Download the needed repositories

Full download (do not have cisst-saw)

• Make a workspace WORKSPACE_NAME and navigate to it

• mkdir src and navigate to it

• git clone https://github.com/jhu-cisst/cisst-saw --recursive

• cd cisst-saw

• git submodule foreach git checkout devel

• git submodule foreach git pull

• git submodule foreach git submodule init

• git submodule foreach git submodule update

• under "cisst-saw/sawRobotIO1394/components/code/Amp1394", do "git checkout devel", "git pull"

• This step is specific to Vanderbilt University force sensor setup except the last note

  • Under "cisst-saw/sawATIForceSensor/":
  • add an origin-arma to have arma force sensor specifics, "git remote add origin-arma https://github.com/wanglong06/sawATIForceSensor.git"
  • do "git branch VU", then "git pull origin-arma VU"
  • If you are not at VU, you still need to edit atinetft_xml.cpp to allow for roslaunch capability see https://github.com/wanglong06/sawATIForceSensor/blob/VU/ros/src/atinetft_xml.cpp copy lines 49-53

• build it using "Compiling" instructions below

• cd WORKSPACE_NAME/src

• git clone https://github.com/jhu-dvrk/dvrk-ros.git

• cd dvrk-ros,

• git checkout devel

• git pull

• catkin build

• git clone https://github.com/wanglong06/continuous_palpation.git

Partial download (already have nri)

• cd WORKSPACE_NAME/src
• git clone https://github.com/wanglong06/continuous_palpation.git

Compiling (first time setup)

• cd to base dir "catkin_ws_xxxx"
• catkin init
• catkin config --profile release -x _release
• catkin profile set release
• catkin config --cmake-args -DCMAKE_BUILD_TYPE=Release
• catkin build

To run the code

First time setup

• Open MATLAB to the continuous_palpation folder. Open Matlab_scripts/dvrk_init_continuous_palp.m
• Edit the line defining the dvrk_nri_matlab path if necessary (line 9)

Define palpation boundary

• Turn on the robot (presumably launching teleop would work too, but I used this) eg:

roscore
rosrun dvrk_robot dvrk_console_json -j /home/arma/catkin_ws/src/cisst-saw-nri/sawIntuitiveResearchKit/share/vu-dVRK/console-PSM2_VU.json

• Home the robot
• In MATLAB, run 'GenPath/DefineExplorationMapBoundary.m' and follow directions
• If you want to use the map you just saved, make sure to edit 'Matlab_scripts/Main_RAL_Continuous_Palpation.m' to set the 'RasterTrajName' variable

Running continuous palpation

• Turn on force sensor if needed (VU needs to run xPC force sensor)
• source your workspace
• In two separate terminals type:

roslaunch continuous_palpation continuous_palpation.launch

and

rosbag record --split --duration=4m -e '(?!/stereo).*|/stereo/right/image_rect|/sreo/right/camera_info|/stereo/left/image_rect|/stereo/left/camera_info' -x /set_continuous_palpation_trajectory -o cont_palp_split

• In MATLAB, run Main_RAL_Continuous_Palpation
  • Make sure to set RasterTrajName to whatever mat file you collected above for the trajectory boundary

GP Results from Data

Continuous palpation - Seeing GP result from txt file (deprecated, but sometimes useful) follow instructions to save data save bags to a folder edit "process_bags_for_GP.py" to set the folder, bagname, and output filename cp outputname.txt current_GP_result.txt Then change the file dvrk_nri_robot on lines 150-151 to use FILE_STREAMING catkin build roslaunch dvrk_nri_robot dvrk_nri_teleop_vu.launch rostopic pub /dvrk/GP/set_GP_running std_msgs/Booldata: true" Run preetham's MATLAB visualizer in matlab /home/arma/catkin_ws/src/cisst-saw-nri/nri/sawNRIModelFW/matlab/ral ral_demo_online.m You can change the GP parameters in cisst-saw-nri/nri/sawNRIModelFW/components/code/GP.cpp ScaleFactor LengthScale