ifthresholds

score ranking the standard threshold methods based on manually labeled images and images produced by various threshold

• The threshold ranking will be based on manually labelled images and images produced by applying the standard threshold methods. IfThreshold guides researchers on which threshold method is the best one for their images:
  • 3 Scoring methods: count method, overlap method, region prop method which includes area, aspect ratio, and circularity comparison.
  • All the scores calculated with images from IGD study is written to a score ranking table and saved as a CSV file.
  • Terminal operation: input your own images and get ranking table and a visual comparison image.

Repository Structure

  |- README.md
  |- ifthresholds/
      |- __init__.py
      |- main.py
      |- score_method.py
      |- write_csv.py
      |- tests/
        |- __init__.py
        |- test_main.py
        |- __pycache__/
      |- data/
        |- ogd.tif
      |- __pycache__/
  |- doc/
      |- README.md
      |- functionality.md
      |- usage_cases.md
  |- examples/
      |- README.md
      |- workbook.ipynb
  |- setup.py
  |- .travis.yml
  |- environment.yml
  |- .pylintrc (for pylint conflict with opencv)
  |- .gitignore
  |- LICENSE

Activating the virtual environment

• Included within the root of the repository is a virtual environment pre-suited to run ifthresholds
  • The virtual environment is located within environment.yml
  • To create the virtual environment from the .yml file: conda env create -f environment.yml
  • To activate the virtual environment: conda activate flashing_lights_env
  • The environment contains:
    • Python 3.7
    • numpy
    • scikit-image
    • scikit-learn

Using flashing_lights

• ifThresholds can be executed through a jupyter notebook or terminal.
  • It is recommended to run the code within the included virtual environment to avoid dependency hell
  • Examples included in jupyter notebooks within ifThresholds/examples/workbook.ipynb that demonstrate how to use the code. To access these notebooks, enter the following into the command line: jupyter notebook ifThresholds/examples/workbook.ipynb

Example Output

Miscellaneous Notes