JPEG DNA BC Transcoder

Bachelor Semester Project: JPEG Transcoding for DNA based storage

École Polytechnique Fédérale de Lausanne, Computer and Communication Sciences

Supervised by Prof. Dr. Touradj Ebrahimi and Davi Lazzarotto

The goal of this project is to study the state of the art in DNA storage and coding, and develop a transcoding module that encodes the quantized DCT coefficients of an already compressed JPEG file with DNA nucleotides, which in turn is then integrated with a DNA sequencing, storage and synthesis simulator. This repository contains the transcoding module which has been built by modifying the software used to encode DNA images - JPEG DNA - developed by the Mediacoding group in the I3S laboratory, in agreement with the standards described by the Jpeg DNA research group in - DNA-based Media Storage - State-of-the-Art, Challenges, Use Cases and Requirements.

Installation

To install the required packages and set up the transcoder you need to have pip and homebrew installed.

First we set up the JPEG_DNA_Transcoder repository:

To install the repository use the following command at the root of the repository’s folder:

pip install -r requirements.txt

To use the commands from the terminal install the following package at the root of the folder:

python setup.py install

Then we set up the Python wrapper for the ibjpeg C library:

brew install libjpeg

pip install Cython

Please update the include and lib paths in setupWrapper.py such that they point to your installation.

libjpeg_include_dir = "path/to/libjpeg/build/include"
libjpeg_lib_dir = "path/to/libjpeg/build/lib"

Tip: Run the following command in order to find the path to libjpeg:

brew info libjpeg

To install the header files needed to build Python extensions: (you can probably skip this step if you already have all the needed developer tools like gcc,...)

pip install python3-dev

Finally, to compile the extension for use in the project’s root directory, run the following in the root of the /Jpeg_DNA_Transcoder directory:

python setupWrapper.py build_ext −−inplace

Functionality

Encoding

To encode a JPEG file into DNA nucleotides you will have to specify the path of your JPEG image and the path on which you would like to store the output DNA sequence.

 python -m jpegdna.scripts.jpegdnargb_encode $IMG_PATH.jpg $DNA_OUT_PATH

Please note that the terminal will print the type of Chroma Subsampling of the JPEG file. You will have to remember this when decoding the DNA sequence.

Decoding

To decode a DNA sequence back to a JPEG file you will have to specify first the type of Chroma Subsampling of the original JPEG image (simply copy the output of the encoder), the path of the DNA sequence, and finally the path on which you would like to store the output decoded PNG file.

python -m jpegdna.scripts.jpegdnargb_decode $SUBSAMPLING $DNA_IN_PATH $IMG_OUT_PATH.png

Example for first parameter: $SUBSAMPLING = 4:2:0

Credit:

The original JPEG DNA software can be found on Jpeg_DNA_Python. Check its LICENSE.md document in the root of this project.
The adapted python wrapper can be found on dct-coefficient-decoder.