This repository shares the python tools published in "Skeletonizing the Dynamics of Soft Continuum Body from Video" (https://www.liebertpub.com/doi/full/10.1089/soro.2020.0110).

@article{inoue2021skeletonizing,
  title={Skeletonizing the Dynamics of Soft Continuum Body from Video},
  author={Inoue, Katsuma and Kuniyoshi, Yasuo and Kagaya, Katsushi and Nakajima, Kohei},
  journal={Soft Robotics},
  year={2021},
  publisher={Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd Floor New~…}
}

Skeletonizing soft body

Please run the following script for extracting centerline(s) of soft body recorded in your video.

$ python src/script/extract_centerline.py
    [-h] [--reset_cache]
    [--warp_threshold WARP_THRESHOLD]
    [--skeleton_num SKELETON_NUM]
    [--frame_offset FRAME_OFFSET]
    [--frame_end FRAME_END]
    [--resize_rate RESIZE_RATE]
    [VIDEO_PATH]

The extracted data will be saved on [VIDEO_PATH]/raw.pkl as default right after terminating the script.

Optional arguments


`--reset_cache`	clearing the saved data (raw.pkl)
`--warp_threshold [float]`	threshold for pausing script when detecting warped pathes (default: inf).
`--skeleton_num [int]`	# of extracted path (default: 1)
`--frame_offset [int]`	setting the offset position (default: 0)
`--frame_end [int]`	setting the end position (default: None)
`--resize_rate [float]`	setting the resize rate of video (default: 1.0)

Console commands


`Space`	pausing / resuming the script
`Ctrl-c` or `ESC`	terminating the script with saving the extracted paths.
`Enter`	launching the image editor GUI (when paused)
`m`	launching the ROI editor GUI (when paused)
`r`	moving to the offset frame (when paused)
`x`	moving to the next frame (when paused)
`z`	moving to the previous frame (when paused)

ROI editor

ROI and HSV parameters used in the background subtraction process can be edited as follows.

Image editor

Extracted image by background subtraction can be edited as follows.


distance	displaying the distance field
travel	displaying the traveling time field
fix h	fixing the height (horizontal position) of the basal point
fix w	fixing the width (vertical position) of the basal point


α	constant value adjusting the convexity of the speed vector field (default: 0.5)
θ_T	boundary threshold for calculating the traveling time field (default: -1.0)
δ	step width used in gradient-descent process (default: 1.0)
ε_b	maximum distance between the current and previous basal point (used in the basal point estimation)
ε_t	maximum distance between the current and previous tip point(s) (used in the tip point(s) estimation)
θ_min	minimum distance between estimated tip points and the edge of the extracted area (default: 0.0).

Visualization

The following scripts create_smoothed_data.py and create_output_movie.py visualize the extracted paths with colormaps and overlaid video from the data stored in [VIDEO_PATH]/raw.pkl, respectively.

# Outputting colormaps on [VIDEO_PATH]/smoothed.pdf
# Also smoothed pathes will be saved on [VIDEO_PATH]/smoothed.pdf
$ python src/script/create_smoothed_data.py [VIDEO_PATH]

# rendering overlaid video on ```[VIDEO_PATH]/movie.mp4
# ffmpeg is required to create the video
$ python src/script/create_output_movie.py [VIDEO_PATH]

Short snippet to read data

Also, you can use the following codes to read the extracted data.

import joblib

path = "[VIDEO_PATH]/raw.pkl"
# path = "[VIDEO_PATH]/smoothed.pkl"

with open(path, mode="rb") as f:
    result_data = joblib.load(f)

Installation

for Ubuntu or MacOS (recommended)

Requirements (recommended)

pyenv
pipenv

Please install the following dependencies for pyenv setup

$ sudo apt install -y make build-essential libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev

Next, download pyenv

$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv
$ git clone git://github.com/yyuu/pyenv-update.git ~/.pyenv/plugins/pyenv-update

Then, please add the following scripts in .bashrc or .zshrc

export PYENV_ROOT="$HOME/.pyenv"
export PATH="$PYENV_ROOT/bin:$PATH"
eval "$(pyenv init -)"

Now, it's time to download the python kernel

$ pyenv update
$ pyenv install anaconda3-2020.02
$ pyenv local anaconda3-2020.02
$ pip3 install --user pipenv

Especially, please install anaconda3-2020.02 to run this program.

$ pyenv install anaconda3-2020.02
$ conda install -c conda-forge pipenv
$ pipenv --python=$(conda run which python) --site-packages
$ pipenv install
$ pipenv shell

for Windows 10

We recommend to use anaconda3 environment and install the following packages

dill==0.3.1.1
multiprocess==0.70.9
numpy==1.18.1
opencv-contrib-python==4.2.0.32
opencv-python==4.2.0.32
parse==1.14.0
pathos==0.2.5
pox==0.2.7
ppft==1.6.6.1
scikit-fmm==2019.1.30
six==1.14.0

ASmallSquishySquid/soft_skeleton_solver