PRFina / pyRinocitologia

a comparative study on nasal cytology techniques using image analysis for my BSc thesis

pyRinocitologia

Central repository for Rinocitologia project developed as an undergraduate thesis. The purpose of this repository is to contains all development code allowing...

Design Philosophy

• Reproducibility
• Process automation
• Explicit is better than implicit
• Infrastructure built around data
• Prefer cross-platform solution

Directory Structure

.
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+--- data                       data used by code 
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+--- models                     pre-trained models and stored weights
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+--- notebooks                  jupyter notebooks for analisys and experiments
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+--- report                     resources used for documentation 
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+--- src                        main code
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+--- tools                      code for misc utilities
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+--- config.ini.example         configuration file  
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+--- README.md
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+--- requirements.txt           python pip dependencies file

Setup

• Create a virtual environment with conda or virtualenv (optional but recommended)

• Install dependencies:

pip install -r requirements.txt

• Setup the environment with config.ini, rename config.ini.example into config.ini and change content to adapt to your environment

Use

You can use your custom data or use our Open Data Dataset. dataset/s could be clone directly in the main repository.

Data Gathering

Execution Flow

Tools

Various utilities script has been developed.

• metadata_generator.py is a small command line utility to help in generate a dataset metadata json file. for more info:

python metadata_generator.py --help

note:

image annotation tool : VGG Image Annotation (VIA)

Warnings

The python interpreter cwd (Current Working Directory) must be set to the root directory/parent directory of /src folder eg:

import os
os.chdir("..")

or equivalently, call python interpreter from the parent directory:

python <parent dir>/src <script name>

or add to PYTHONPATH the parent directory:

export PYTHONPATH=<root directory>
python <script name>

(if you use pyCharm IDE this is done automatically in run configuration)

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