AnnoLib

AnnoLib is a simple yet very powerful library for converting between Annotation Dataformats. To be able to read and write between n formats, programmers only need to implement n readers and n writers, instead of n(n-1) conversion classes.

Getting Started

AnnoLib uses an intermediate representation of annotations, defined as AnnoDatabase datatype. Readers are required to parse the input into AnnoDatabase and Writers are required to accept AnnoDatabase and be able to write to its own format. This decouples Readers from Writers and help programmers to code independently from each others.

Prerequisites

Python3

sudo apt install python3

Pip

curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py --user

Installing

Change the directory to root project folder

cd /AnnoLib/annolib

Compile the source code

python3 setup.py develop

Deployment

From the perspective of a library user, you only need to initiate a reader, pass it to writer then call write() function

parser = MySQLParser("utf-8",
                        "~/Desktop/PointCloudISU/WebApp/www/html/sds_images",
                        "~/Desktop/PointCloudISU/sdsgwas/src/traing_data")
writer = CSVTrainTestWriter(parser, 0.8, False)
writer.set_output_file("train.csv", "test.csv")
writer.write()

From the perspective of a library writer, you only need to subclass AnnoParser or AnnoWriter for reader and writer respectively. Each of those classes is an Abstract Base Class so instead of fail silently, it will throw error if you implement your subclass wrong

class AnnoParser(metaclass=ABCMeta):
    """Abstract class for xml parser and matlab file parser"""

    def __init__(self, encoding: str) -> None:
        self.encode_method = encoding
        self.shapes: AnnoDatabase = []
        super().__init__()

    @abstractmethod
    def parse_anno(self) -> AnnoDatabase:
        """
        abstract method, will be implemented diffirently by children
        parse annotation either form .xml file or matlab json file
        """
        pass

    @property
    def anno_data(self) -> AnnoDatabase:
        """
        smart getter, just call my_parser.Anno_Data, it will check
        if ParseAnno has run yet and return annotation data.
        self.shapes = [{'bbox' =[(x1, y1, x2, y2, 'label')], 'img_path' = ''}]

        """
        # Empty List valuates to fall
        if self.shapes:
            return self.shapes
        self.shapes = self.parse_anno()
        return self.shapes

Built With

• Setuptools - A packaging solution for Python project

Contributing

We follow Iowa State University authorship policy, please send requests to us at the address: [email protected]

Versioning

We use git for versioning. For the versions available, use the git tagging.

Authors

• Truong Tran - LinkedIn

See also the research project info at lab website for detail information.

License

Copyright 2018 Baskar Ganapathysubramanian, all rights reserved

Acknowledgments

We gratefully acknowledge support from Plant Science Institute at Iowa State University.