Endo-Depth-and-Motion

This repository contains the code of Endo-Depth's depth prediction from single images, the photometric and the others trackings methods and the volumetric fusion used in the paper

Localization and Reconstruction in Endoscopic Videos using Depth Networks and Photometric Constraints

David Recasens, José Lamarca, José M. Fácil, José María M. Montiel and Javier Civera

I3A, University of Zaragoza

RA-L paper
arXiv paper
IROS 2021 video presentation

Full video of Endo-Depth-and-Motion working on Hamlyn dataset

@article{recasens2021endo,
  title={Endo-Depth-and-Motion: Reconstruction and Tracking in Endoscopic Videos Using Depth Networks and Photometric Constraints},
  author={Recasens, David and Lamarca, Jos{\'e} and F{\'a}cil, Jos{\'e} M and Montiel, JMM and Civera, Javier},
  journal={IEEE Robotics and Automation Letters},
  volume={6},
  number={4},
  pages={7225--7232},
  year={2021},
  publisher={IEEE}
}

💭 About

Endo-Depth-and-Motion is a pipeline where first, pixel-wise depth is predicted on a set of keyframes of the endoscopic monocular video using a deep neural network (Endo-Depth). The motion of each frame with respect to the closest keyframe is estimated by minimizing the photometric error, robustified using image pyramids and robust error functions. Finally, the depth maps of the keyframes are fused in a Truncated Signed Distance Function (TSDF)-based volumetric representation.

⚙️ Setup

We have ran our experiments under CUDA 9.1.85, CuDNN 7.6.5 and Ubuntu 18.04. We recommend create a virtual environment with Python 3.6 using Anaconda conda create -n edam python=3.6 and install the dependencies as

conda install -c conda-forge opencv=4.2.0
pip3 install -r path/to/Endo-Depth-and-Motion/requirements.txt

Install PyTorch 1.7.0 accordingly with your Cuda version (see PyTorch website for more alternatives).

# CUDA 11.0
pip install torch==1.7.0+cu110 torchvision==0.8.0+cu110 torchaudio==0.7.0 -f https://download.pytorch.org/whl/torch_stable.html

# CUDA 10.2
pip install torch==1.7.0 torchvision==0.8.0 torchaudio==0.7.0

# CUDA 10.1
pip install torch==1.7.0+cu101 torchvision==0.8.0+cu101 torchaudio==0.7.0 -f https://download.pytorch.org/whl/torch_stable.html

# CUDA 9.2
pip install torch==1.7.0+cu92 torchvision==0.8.0+cu92 torchaudio==0.7.0 -f https://download.pytorch.org/whl/torch_stable.html

💾 Data

The Hamlyn rectified images, the rectified calibration and the ground truth used to train and test the Endo-Depth models can be found here. The ground truth has been created with the stereo matching software Libelas. The rectified color images are stored as uint8 .jpg RGB images and the depth maps in mm as uint16 .png. During the evaluation, pixel values lower than 1 and higher than 300 mm were ignored.

The Hamlyn data used to test the tracking and the volumetric fusion is here. The color and depth images are slightly cropped to avoid the small distortions of the depth Endo-Depth produces at the borders. The depth was computed using the stereo Endo-Depth models and it is in [mm] and in image format uint16. The saturation depth is 300 [mm]. You can also replace it with your own data.

🧠 Endo-Depth

To predict the depth for a single or multiple images use

python apps/depth_estimate/__main__.py --image_path path/to/image_folder --model_path path/to/model_folder

You have must have already download the Endo-Depth model you want to use. If you prefer to store the depth predictions in another folder use the argument --output_path. You can also select the type of the output with --output_type which is set by default to grayscale (grayscale depth images), but you can also choose color (colormapped depth images). By default, the saturation depth is set to 300 [mm], you can change this limit using --saturation_depth. Also, the image depth scaling is by default 52.864 because for Hamlyn dataset the weighted average baseline is 5.2864. This number is multiplied by 10 because the imposed baseline during training is 0.1. The image extension to search for in folder can be changed with --ext (now set as jpg), and you can disable CUDA using the argument --no_cuda.

👀 Tracking

You can execute our photometric tracking with

python apps/tracking_ours/__main__.py -d cuda:0 -i path/to/hamlyn_tracking_test_data -o apps/tracking_ours/results

being -i the input path to the folder containing the different video folders, -o the output path where the odometry in format .pkl is saved. If you want to run the script on CPU instead of on GPU just remove the argument -d cuda:0. The ratio frame-keyframe and number of floors of the pyramid are set to 2 by default, but they can be changed with the arguments -fr and -st, respectively. The output odometries of the Hamlyn test data using our tracking can be found here.

To use alternatively the tracking methods of Open3D run

python apps/tracking_open3d/__main__.py -d cuda:0 -i path/to/hamlyn_tracking_test_data -o apps/tracking_open3d/results -t park

The tracking method can be changed modifying the argument -t: point-to-point (ICP point-to-point), point-to-plane (ICP point-to-plane), steinbrucker (photometric) and park (hybrid photometric and geometric). Additionally, with the argument -r you can execute a global registration with RANSAC to compute a pre-translation between two point clouds before calculating the final translation with the local registration.

The dataset folder structure should be as follows:

   dataset_folder   
      -->rectified01      
         -->color	 
	 -->depth	       
	 -->intrinsics.txt	       
      ...

Tips for the visualization. When the two windows (images and 3D map) display, left click on the middle of the images window and then you can use the following commands pressing the buttons:

a: to start the automode. The currently displayed scene will be tracked and viewed in real time in the 3D window.
s: to stop the automode. This can only be done when one frame is finally tracked and before the next one is started. So just smash the button multiple times until it stops!
h: to print help about more commands, like skip the scene or to track frame by frame.

♻️ Volumetric fusion

In order to get the refined 3D map, you can fuse the registered pseudo-RGBD keyframes obtained from Endo-Depth and the tracking with

python apps/volumetric_fusion/__main__.py -i apps/tracking_ours/results/test1.pkl -o path/to/hamlyn_tracking_test_data/test1

where -i is the input odometry in format .pkl computed with the tracking. The output 3D meshes of the Hamlyn test data using the volumetric fusion are here.

👩‍⚖️ License

Endo-Depth-and-Motion is released under GPL-3.0 License. The code in the folder apps/depth_estimate is property of the authors of Monodepth2 and has its own License.