nyxus_benchmark

This repo is based on code [https://github.com/sameeul/nyxus_benchmark] by Sameeul

The requirements.txt file lists all the required top-level dependencies. To install them, use pip install -r requirements.txt.

There are two classes DatasetGenerator and Benchmark. DatasetGenerator can be initialized like the following:

dataset_generator = DatasetGenerator(   int_image_dir,
                                        seg_image_dir,
                                        base_mask_image_path,
                                        base_intensity_image_path)

Once initialized, an image pair can be created like the following:

dataset_generator.generate_image_pair(n_roi ,roi_size, padding, percent_oversized_roi)

Once image pairs are generated, the benchmark data can be gathered using the Benchmark class.

benchmark = Benchmark(  int_image_dir,
                        seg_image_dir,
                        work_dir, 
                        nyxus_executable, 
                        feature_list, 
                        generate_missing_image
                    )


benchmark.run_benchmark_suit()

After running benchmark data, h1, h2 and h3 header from the performance reporting csv can be used to generate the plot like the following:

benchmark.create_benchmark_plot("Total", "All", "All")

main.py file has a complete working example.