# Project Folder Structure

This document outlines the folder structure of the project and the purpose of each main folder and sub-folder. Below is a detailed description of what each directory contains and its significance in the project.

## source_code

Contains all the source code files for the project. It is where the main functionality of the project is implemented.

## data

This directory stores various types of data used and generated by the project. It includes:

- edge_lists

    Contains lists of edges used in graph-based analyses.

- original_positions

    Stores data on the original positions of elements or nodes before any processing, usually created during simulations.

- reconstructed_positions

    Holds the positions of nodes after they have been reconstructed

- pixelgen_data

    Contains pixelgen data

- slidetag_data

    Contains slidetag data

- colorfolder

    Stores color code data, potentially used for visualization or categorization.

## results

This directory is dedicated to storing the output of analyses and computations. It includes:

- individual_spatial_constant_results

    Results from spatial constant analyses on individual elements.

- plots

    A comprehensive collection of plots generated from the project’s data. It includes:

    - main_spatial_coherence_results

        Summary folder of running the spatial coherence algorithm. It contains spatial constant analysis, correlation dimension prediction and rank gram matrix analysis. Also can contain the reconstructed images.

    - original_image

        Plots of original images before processing.

    - reconstructed_image

        Plots showing images after reconstruction.

    - shortest_path_heatmap

        Heatmaps of shortest paths within networks or graphs.

    - mst_image

        Images showing the minimum spanning tree of a graph.

    - correlation_euclidean_sp

        Plots correlating Euclidean distances and shortest paths.

    - main_spatial_coherence_results

        Results highlighting the spatial coherence in the data.

    - spatial_constant

        A series of plots related to spatial constants, including variations, graph growth analyses, and subgraph sampling.

    - predicted_dimension

        Plots related to the dimensionality predictions of data or networks.

    - clustering_coefficient, degree_distribution, shortest_path_distribution, weight_distribution

        Statistical distributions and analyses related to the graph properties.

- all_subgraphs_reconstruction

    Contains results from reconstructing all subgraphs, including positions and images.

## Miscellaneous

- pixelgen_quality_plots

    Plots assessing the quality of pixel generation.

- bfs_animation

    Animations created using a Breadth-First Search algorithm, showcasing the process or results.

- profiler

    Performance profiling results of the project’s code or algorithms.