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

data
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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
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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
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- 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.


