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crop_image

Small repository to store the cropping step of the BGNN Fish project

https://github.com/hdr-bgnn/crop_image

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Small repository to store the cropping step of the BGNN Fish project

Basic Info
  • Host: GitHub
  • Owner: hdr-bgnn
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 16.1 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 1
  • Open Issues: 3
  • Releases: 4
Created over 3 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

DOI

Crop_image

Small repository to store the "cropping" step of the BGNN project.

This repo is linked to main BGNN Core Workflow that encompasses a complete analysis workflow. It contained the code for the "Cropping" part see here. It is easier to understand the purpose this code and its application if you are familar with BGNN_Snakemake repo.

1 - Short description

input original fish image

Cropped output Cropped fish image

2 - Usage

Input example : + fish image .jpg see INHSFISH000742.jpg + Metadata.json see INHSFISH000742.json

Ouput : + Cropped image .jpg [see INHSFISH000742cropped.jpg]Testdata/INHSFISH000742_cropped.jpg)

Usage in python you need the environment define by crop_env.yml. I suggest to use anaconda or miniconda as environment manager

Crop_image_main.py [-h] [--increase] input_image imput_metadata output

Example using the Test_data with 10% increase in size

Crop_image_main.py INHS_FISH_000742.jpg INHS_FISH_000742.json INHS_FISH_000742_cropped.jpg --increase 0.10

The --increase parameter defines the fractional increase of the bounding box from the original metadata size in each direction (10% in this example). The default value in 0.05.

3 - Container and test

The container can be download here:

``` docker pull ghcr.io/hdr-bgnn/crop_image:latest

or

singualarity docker://ghcr.io/hdr-bgnn/crop_image:latest ```

Container Usage:

In this section the name of the container "cropimage0.0.2.sif" will depend on the version you are downloading or the name you give to container .sif

The usage can be display like this:

singularity run crop_image_0.0.2.sif

To execute the code on the test images test data, run the following

singularity exec crop_image_0.0.2.sif Crop_image_main.py Test_data/INHS_FISH_000742.jpg Test_data/INHS_FISH_000742.json Test_data/INHS_FISH_000742_cropped_test.jpg

Owner

  • Name: Biology Guided Neural Networks
  • Login: hdr-bgnn
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.0.0
date-released: "2023-05-30"
abstract: "Crop_Image is a small repository to store the cropping step of the BGNN Minnow_Segmented_Traits project. This repo is linked to main BGNN Core Workflow that encompasses a complete analysis workflow. It contained the code for the cropping part."
authors:
  - family-names: Tabarin
    given-names: Thibault
    orcid: "https://orcid.org/0000-0003-4256-849X"
  - family-names: Bradley
    given-names: John
    orcid: "https://orcid.org/0000-0003-3858-848X"
  - family-names: Lapp
    given-names: Hilmar
    orcid: "https://orcid.org/0000-0001-9107-0714"
identifiers:
  - description: "Snapshot of Crop_image: Version 0.0.4"
    type: doi
    value: 10.5281/zenodo.7987485
keywords:
  - "imageomics"
  - "image"
license: MIT
repository-code: "https://github.com/hdr-bgnn/Crop_image"
title: "Crop image"
version: 0.0.4

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Dependencies

.github/workflows/Deploy_Crop_Image.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action ad44023a93711e3deb337508980b4b5e9bcdc5dc composite
  • docker/login-action f054a8b539a109f9f41c372932f1ae047eff08c9 composite
  • docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite
Dockerfile docker
  • ubuntu 20.04 build