pyamiimage

pyamiimage is a set of tools to extract semantic information from scientific diagrams.

The current goal is to extract terpene synthase pathway diagrams. 'Extraction' means that we will go from pixel values in an image to a 'smart diagram'. The output of pyamiimage is an image with annotations of substrate, products and enzymes.

We are working to add more support for open formats that encode chemical/pathway information such as CML and GPML.

Installation

Tesseract

To run pyamiimage on your local system you need to have Tesseract installed. If you don't have Tesseract installed, install it from here.

pip install pyamiimage

Usage

pyamiimage is a command-line tool and can be accessed via the terminal or command prompt. To bring up the help run:

pyamiimage --help

You can also include pyamiimage in your program using the provided classes.

AmiImage

AmiImage class provides methods for image manipulation.

from pyamiimage.ami_image import AmiImage

gray = AmiImage.create_grayscale_from_file(image_file_path)

AmiGraph

AmiGraph class generate a graph from arrows in a diagram.

AmiOCR

AmiOCR class provides methods to extract words from the iamge. Uses Tesseract.

Timeline

merged main into nodes_and_pixels and re-branched