This contains source code for autonomated surgical debridement.
Supplemental website with videos: https://sites.google.com/view/calib-icra/
(The following text was written by Sanjay Krishnan.)
The base directory structure for da Vinci utilities. This repository defines the basic structure and utilities for the Da Vinci surgical robot in the AUTOLAB at UC Berkeley.
Starting up the robot
Move the robot arms so they have at least a 1cm box of clearance around the tool tip, make sure that the tool tip is out of the cannula. Open a terminal and run
Create a new tab and run
A teleop interface should load. In the telop interface, click the radio button for Home. You will hear a nasty fan sound from the PSM1 controller, don't worry about this (Sanjay is being negligent right now). Wait until the messages stop and then run Teleop. The robot is now engaged. Do not move the arms unless the clutch is engaged.
Setting up your development environment
If this your first time on davinci0, create a directory for yourself in the home directory. Open a terminal and type
mkdir awesome_autolab_grad cd awesome_autolab_grad
Then, create a virtual environment inside this directory
virtualenv -p /usr/bin/python --system-site-packages my-new-project
This creates a new sub directory that will contain your project. Then, run following command:
cd my-new-project && source bin/activate
You know you are successful when your terminal prompt changes to something like (my-new-project)davinci0@davinci0. NEVER install anything outside your virtual environment. Inside the project directory clone the bare skeleton repository:
git clone --bare https://github.com/BerkeleyAutomation/davinci-skeleton.git
Go to your own github and create a new repository, don't initialize it with anything. For example https://github.com/sjyk/my-new-project.git. Then, run the following commands:
cd davinci-skeleton.git git push --mirror https://github.com/sjyk/my-new-project.git
Then, delete the skeleton repository:
cd .. rm -rf davinci-skeleton.git/
You can now clone your own repository:
git clone https://github.com/sjyk/my-new-project.git cd my-new-project
Commit and push whatever you want to this personal repository.
There are basically three modules that are important (for now) dvrk.robot, config.constants, and autolab.data_collector:
from config.constants import * from dvrk.robot import * from autolab.data_collector import *
First, create a robot object:
psm1 = robot("PSM1")
To move the robot to a home position:
To move the robot's tooltip to a new position:
import tfx #A new position post,rott = ((0.05, 0.02, -0.15), (0.0, 0.0,-160.0)) #creating the proper data structures pos = [post, post, post] rot = tfx.tb_angles(rott, rott, rott) #execute move with a SLERP motion planner psm1.move_cartesian_frame_linear_interpolation(tfx.pose(pos, rot), 0.03)
Talk to Sanjay before using more advanced features of the API (all of which are in dvrk.robot).
Unique experimental identifiers are useful, and every time you create a DataCollector class (which arbitrates the sensor readings) it creates a new one for you.
d = DataCollector() print(d.identifier) >>> 80PTSJF68HLISWKQY1ZL
This can be used to make a directory in the results folder:
import os try: os.stat('results/'+d.identifier) except: os.mkdir('results/'+d.identifier)
This folder is a good place to put all of your experimental data.
If you run the program scripts/runExp.sh it will execute the main program and commit the config, parameters, and results to github:
(my-new-project)davinci0@davinci0:~/davinci-skeleton$ bash scripts/runExp.sh PID of running experiment 9666 Thu Jul 6 12:04:24 PDT 2017 Still working...log in: 0 /tmp/exp.Y8cir8gwG Thu Jul 6 12:04:25 PDT 2017 Still working...log in: 0 /tmp/exp.Y8cir8gwG
It logs all standard error and out to a temporary directory and prints out the PID (really useful if something goes wrong and you want to kill). The cool part is that even if you kill the python program the bash script will commit whatever intermediate results to github so you won't lose them!