xiaosnowqiang / SDF_based_assistance

Improving Surgical Situational Awareness with Signed Distance Field

Paper

Framework to design and evaluate image-guided navigation systems for surgery presented in our paper at IROS 2023, Improving Surgical Situational Awareness with Signed Distance Field: A Pilot Study in Virtual Reality.

If you found this work helpful, please reference us using the following citation:

@misc{ishida2023improving,
      title={Improving Surgical Situational Awareness with Signed Distance Field: A Pilot Study in Virtual Reality}, 
      author={Hisashi Ishida and Juan Antonio Barragan and Adnan Munawar and Zhaoshuo Li and Andy Ding and Peter Kazanzides and Danielle Trakimas and Francis X. Creighton and Russell H. Taylor},
      year={2023},
      eprint={2303.01733},
      archivePrefix={arXiv},
      primaryClass={cs.HC}
}

Overview

The virtual reality drilling simulator is able to actively modify anatomy with a virtual drill. The simulator has both VR and haptics integration as well as the ability to generate data for use in downstream algorithm development. Volumetric_drilling is a plugin built on top of Asynchronous Multibody Framework (AMBF) developed by Munawar et al. We show the use of the plugin in lateral skull base surgery.

1. Installation Instructions:

Lets call the absolute location of this package as <volumetric_plugin_path>. E.g. if you cloned this repo in your home folder, <volumetric_plugin_path> = ~/volumetric_drilling/ OR /home/<username>/volumetric_plugin

1.1 Install and Source AMBF 2.0

Clone and build ambf-2.0 branch.

git clone https://github.com/WPI-AIM/ambf.git
cd ambf
git checkout -b ambf-2.0 origin/ambf-2.0
git pull

Note that depth and image recording are enabled by default (in camera ADFs) and these features only work on Linux with ROS installed. Additionally, the following packages must be installed prior to building to AMBF:

cv-bridge # Can be installed via apt install ros-<version>-cv-bridge
image-transport # Can be installed via apt install ros-<version>-image-transport

Build and source ambf (make sure you're on branch ambf-2.0 before building) as per the instructions on AMBFs wiki: https://github.com/WPI-AIM/ambf/wiki/Installing-AMBF.

1.2 Clone and Build Simulator

git clone https://github.com/LCSR-SICKKIDS/volumetric_drilling
cd <volumetric_plugin_path>
mkdir build
cd build
cmake ..
make

If everything went smoothly, we are good to go.

2 Running the Plugin with ambf_simulator:

The volumetric drilling simulator is a plugin that is launched on top of the AMBF simulator along with other AMBF bodies, described by AMBF Description Format files (ADFs), as will be demonstrated below. The libvolumetric_drilling.so plugin is initialized in the launch.yaml file and can be commented out for the purpose of debugging the ADF files.

Below are instructions as to how to load different volume and camera options. The -l tag used below allows user to run indexed multibodies that can also be found in the launch.yaml under the multibody configs: data block. More info on launching the simulator can be found in the AMBF Wiki:

https://github.com/WPI-AIM/ambf/wiki/Launching-the-Simulator
https://github.com/WPI-AIM/ambf/wiki/Selecting-Robots
https://github.com/WPI-AIM/ambf/wiki/Command-Line-Arguments

Note that the executable binary,ambf_simulator, is located in ambf/bin/lin-x86_64 and you must be in that folder to run the simulator.

2.1 Different Volume Options

We provide three different volumes to choose from:

Option 1:

A low res volume (1) and a drill (0):

cd ambf/bin/lin-x86_64/
./ambf_simulator --launch_file <volumetric_plugin_path>/launch.yaml -l 0,1

Option 2:

A medium res volume (2) and a drill (0):

cd ambf/bin/lin-x86_64/
./ambf_simulator --launch_file <volumetric_plugin_path>/launch.yaml -l 0,2

Option 3:

A high res volume (3) and a drill (0):

cd ambf/bin/lin-x86_64/
./ambf_simulator --launch_file <volumetric_plugin_path>/launch.yaml -l 0,3

Option 4: User-provided volume

Patient specific anatomy may also be used in the simulator. The volumes are an array of images (JPG or PNG) that are rendered via texture-based volume rendering. With images and an ADF for the volume, user specified anatomy can easily be used in the simulator. We provide utility scripts (located in the scripts folder) that can convert both segmented and non-segmented data from the NRRD format to an array of images.

2.2 Camera Options:

Different cameras, defined via ADF model files, can be loaded alongside the simulation.

Option 1:

You can add 4 to any of the above commands to load a segmentation_camera. This camera publishes a segmented depth point cloud. Launch example:

cd ambf/bin/lin-x86_64/
./ambf_simulator --launch_file <volumetric_plugin_path>/launch.yaml -l 0,1,4

Option 2:

You can add 5 to any of the above commands to load two cameras (one of each stereo eye). Each of these cameras publishes a its video. Launch example:

cd ambf/bin/lin-x86_64/
./ambf_simulator --launch_file <volumetric_plugin_path>/launch.yaml -l 0,1,5

Option 1 and 2 combined:

You can also load both the segmentation_camera and the two stereo_cameras together as:

cd ambf/bin/lin-x86_64/
./ambf_simulator --launch_file <volumetric_plugin_path>/launch.yaml -l 0,1,4,5

2.3 Changing Scene Parameters

All the relevant ADF scene objects are in the ADF folder and can be modified as needed. For example, camera intrinsics can be adjusted via the field view angle and image resolution parameters of Camera ADFs.

2.4 Manipulating Drill

The virtual drill can be manipulated via a keyboard or haptic devices such as the Geomagic Touch/Phantom Omni.

2.4.1 Keyboard Navigation

#	Linear Motion of Tool	Description
1	[Ctrl+W]	Moves vertically upward w.r.t. camera
2	[Ctrl+S]	Moves vertically downward w.r.t. camera
3	[Ctrl+A]	Moves horizontally left w.r.t. camera
4	[Ctrl+D]	Moves horizontally right w.r.t. camera
5	[Ctrl+I]	Moves in the forward direction w.r.t camera
6	[Ctrl+K]	Moves in the backward direction w.r.t camera

#	Angular Motion of Tool	Description
1	[Num 8]	Rotates towards upward direction w.r.t tool
2	[Num 5]	Rotates towards downward direction w.r.t. tool
3	[Num 4]	Rotates towards the left direction w.r.t. tool
4	[Num 6]	Rotates towards the right direction w.r.t. tool

#	Miscellaneous	Description
1	[Ctrl+O (letter o)]	Toggle the drill's control mode between Haptic Device / Keyboard to ROS Comm
1	[C]	Changes the size of drill burr/ radius of tip sphere (2 mm, 4 mm, and, 6 mm)
2	[Ctrl+N]	Resets the shape of the volume
3	[Alt+R]	Resets the whole world and this plugin
2	[X]	Toggles the functionality of sudden jumping of drill mesh towards the followSphere
3	[B]	Toggles the visibility of drill mesh in the scene
4	[Ctrl+C]	Toggles the visbility of collision spheres

2.4.2 Geomagic Touch/Phantom Omni

2.5 Navigating in Simulator

Camera movement in the simulator can be accomplished through AMBF's python client, mouse movement or Head Mounted Displays (HMDs)

2.5.1 AMBF Python Client

Camera can be moved with the AMBF python client as described here: https://github.com/WPI-AIM/ambf/wiki/The-Python-Client. To move all cameras in sync the object that should be moved is the parent of all the cameras, main_camera.
Note that only one instance of the AMBF python client can be opened at a time. The data generation script uses the python client, hence camera movement must be added to that script if data is also being recorded.

2.5.2 Mouse Movement

Navigation using mouse shortcuts in AMBF is described here: https://github.com/WPI-AIM/ambf/wiki/Keyboard-and-Mouse-Shortcuts

2.5.3 HMDs

2.6 Data Recording

A python script (scripts/data_record.py) is provided to record data based on the user's configuration. By default, the left and right stereo images, depth point cloud, segmentation mask,drill/camera poses, removed voxels and drill burr changes are recorded. The data is stored as a convenient and well-organized hdf5 file. NOTE:

• Source the ambf and vdrilling_msgs environment in terminal before running the script.
• By default, data recording should be launched after the simulator. We perform sanity check on this to make sure topics subscribed are meaningful.