som-test.py

import numpy as np
import sys, random
from som.som import SOM
from som.topology import Rectangular, Hexagonal
from data.data import Data
from matplotlib import pyplot as plt
from matplotlib import cm
from utility.timer import Time
from settings.somSettings import SOMSettings
from som.neighborhood import GuassianNeighborhood, BubbleNeighborhood, MexicanHatNeighborhood, LinearNeighborhood, CosineNeighborhood, CauchyNeighborhood, EpanechnikovNeighborhood
from nn.scheduler import ExponentialLR, SteppedLR


def dataShift(dims):
    offSet = [1, 0.5, 1]
    diffLen = abs(len(offSet) - dims)
    offSet.extend([0] * diffLen)
    random.shuffle(offSet)
    return offSet[:dims]


# Helper function for plotting dummy data
def scatterPairwise(data, weights, size: float = 10, colors: list[str, str] = ['tab:blue', 'tab:orange']):
    """
    Create a scatter plot of pairwise dimensions of a multidimensional dataset on a grid.

    Parameters:
    data (ndarray): The multidimensional dataset to be plotted.
    size (float): The size of each scatter point in the plot (default 10).
    color (str): The color of each scatter point in the plot (default 'blue').

    Returns:
    None.
    """
    num_dims = data.shape[1]
    fig, axes = plt.subplots(num_dims, num_dims, figsize=(12, 12))

    for i in range(num_dims):
        for j in range(num_dims):
            if i == j:
                axes[i][j].axis('off')
            else:
                axes[i][j].scatter(data[:, i], data[:, j], s=size, c=colors[0], alpha=0.5,label='data')
                axes[i][j].scatter(weights[:, i], weights[:, j], s=1.5*size, c=colors[1], alpha=1,label='weights')
                axes[i][j].set_xlabel(f"Dim {i}")
                axes[i][j].set_ylabel(f"Dim {j}")
                axes[i,j].legend(loc='best', fontsize='small')

    plt.tight_layout()
    plt.show()


def map(values: np.ndarray, arange: list = [0,1]) -> np.ndarray:
    assert len(arange) == 2, 'arange must be of length 2'
    assert arange[0] < arange[1], 'arange must start at a lower value than it ends'

    c, d = arange[0], arange[1]
    a, b = np.min(values), np.max(values)

    return c + ((d - c) / (b - a)) * (values - a)

def plotMatrix(matrix, grid, shape='o', size=1):
    plt.figure(figsize=(12,12))  # specify the figure size in inches
    fig, ax = plt.subplots()

    # create an array of points for the grid
    points = grid

    # plot each point
    values = map(matrix.flatten(), [0,255]).astype('int')
    colors = cm.viridis(values)


    ax.scatter(points[:, 0], points[:, 1], color=colors, s=250*size, marker=shape)

    ax.set_title('Weight Matrix')

    # Increase the size of the plot (or 'zoom out')
    ax.set_aspect('equal', adjustable='box')
    ax.set_xlim(-1, points[:,0].max()+1)
    ax.set_ylim(-1, points[:,1].max()+1)

    plt.show()


def pickNeighborhood(neighborhood: str, scale: float):
    if neighborhood == 'gaussian':
        return GuassianNeighborhood(scale)
    elif neighborhood == 'mexicanhat':
        return MexicanHatNeighborhood(scale)
    elif neighborhood == 'bubble':
        return BubbleNeighborhood(scale)
    elif neighborhood == 'linear':
        return LinearNeighborhood(scale)
    elif neighborhood == 'cosine':
        return CosineNeighborhood(scale)
    elif neighborhood == 'cauchy':
        return CauchyNeighborhood(scale)
    elif neighborhood == 'epanechnikov':
        return EpanechnikovNeighborhood(scale)
    else:
        raise ValueError(f"{neighborhood} is not an option")


def pickTopology(topology: str, gridSize: tuple, numFeatures: int):
    if topology == 'rectangular':
        return Rectangular(gridSize, numFeatures)
    elif topology == 'hexagonal':
        return Hexagonal(gridSize, numFeatures)
    else:
        raise ValueError(f"{topology} is not an option")


def plotPies(grid, title, countSet: int = 0):
    fig, ax = plt.subplots(*grid.gridSize, figsize=(grid.gridSize[1], grid.gridSize[0]))

    # Adjust the subplot parameters to reduce the space between subplots
    plt.subplots_adjust(wspace=0.1, hspace=0.1)

    # Set aspect ratio of all subplots to be equal so that the pie charts look like circles, not ellipses
    for a in ax.ravel():
        a.set_aspect('equal')

    for index, count in enumerate(grid.counts[countSet]):
        xx, yy = np.unravel_index(index, grid.gridSize)
        if np.sum(count) > 0:  # check if there are counts for this neuron
            ax[xx,yy].pie(count)
        else:  # if no counts, you can leave it blank or put something else here
            ax[xx,yy].axis('off')

    plt.suptitle(title)
    plt.show()


def plotBars(grid, countSets = [0, 1]):
    fig, ax = plt.subplots(*grid.gridSize, figsize=(grid.gridSize[1], grid.gridSize[0]))

    # Adjust the subplot parameters to reduce the space between subplots
    #plt.subplots_adjust(wspace=0.1, hspace=0.1)

    # Set aspect ratio of all subplots to be equal so that the pie charts look like circles, not ellipses
    for a in ax.ravel():
        a.set_aspect('equal')

    backgroundColor = grid._umatrix.reshape(*grid.gridSize)
    minValue = backgroundColor.min()
    backgroundColor = backgroundColor - minValue
    maxValue = backgroundColor.max()
    backgroundColor = backgroundColor/maxValue
    counts0 = grid.counts[countSets[0]] / np.sum(grid.counts[countSets[0]], axis=1).reshape(grid.numNeurons,1)
    counts1 = grid.counts[countSets[1]] / np.sum(grid.counts[countSets[1]], axis=1).reshape(grid.numNeurons,1)
    counts = counts0 - counts1

    for index, count in enumerate(counts):
        xx, yy = np.unravel_index(index, grid.gridSize)
        ax[xx,yy].set_ylim(-1,1)
        ax[xx,yy].set_facecolor(f'{backgroundColor[xx,yy]}')
        ax[xx,yy].bar(np.arange(len(count)), count)

    plt.suptitle("Count Deltas")
    plt.show()

if __name__ == "__main__":
    settings = SOMSettings()
    try:
        configFile = sys.argv[1]
        settings.getConfig(configFile)
        settings.setConfig()
    except IndexError:
        pass
    print(settings)

    # Initialize a timer to measure the runtime of different parts of the code
    timer = Time()

    print("Importing data...\n")
    timer.start()
    data = Data(trainAmount=settings['trainAmount'], evalAmount=settings['validAmount'], batchSize=settings['batchSize'], dataPath=settings['dataPath'], normalize=settings['normalize'])
    data.inputFeatures(*settings['features'])
    data.importData(*settings['dataFiles'])
    print(data)
    timer.record("Importing Data")

    # Create and initialize the Self-Organizing Map (SOM)
    timer.start()
    grid = SOM(settings['learningRate'], settings['gridSteps'], settings['decreaseEvery'])

    grid.setComponent(pickTopology(settings['topology'], settings['gridSize'], data.trainSet.shape[-1]))
    grid.setComponent(pickNeighborhood(settings['neighborhood'], settings['scale']))
    if settings['scheduler'] == 'exponential':
        grid.setComponent(ExponentialLR(grid, settings['decayrate']))
    elif settings['scheduler'] == 'stepped':
        grid.setComponent(SteppedLR(grid, settings['decayrate'], settings['stepSize']))
    timer.record("SOM setup")


    # Train the SOM using the test data
    timer.start()
    print('beginn training...')
    grid.train(data.train, settings['epochs'])
    timer.record("Training")

    timer.start()
    print('beginn evaluation...')
    grid.eval(data.train)
    grid.eval(data.eval)
    timer.record("Evaluation")

    # Visualize the SOM and U-Matrix
    if grid.topology.numFeatures == 2:
        # If the data has only two dimensions, create a simple scatter plot
        plt.scatter(data.trainSet.data[:,0],data.trainSet.data[:,1],label='data')
        plt.scatter(grid.weights[:,0],grid.weights[:,1],label='weights')
        plt.legend()
        plt.show()
    else:
        # If the data has more than two dimensions, create a scatter plot of pairwise dimensions
        scatterPairwise(data.trainSet.data, grid.weights)

    if settings['topology'] == 'hexagonal':
        plotMatrix(grid.weightMatrix, grid.topology.gridIndices,'H',1.5)
        plotMatrix(grid.uMatrix, grid.topology.gridIndices,'H',1.5)
    else:
        plotMatrix(grid.weightMatrix, grid.topology.gridIndices,'s')
        plotMatrix(grid.uMatrix, grid.topology.gridIndices,'s')

    #plotPies(grid, "Train Seit", 0)
    #plotPies(grid, "Eval Set", 1)
    #plotBars(grid)

    # Print the total runtime of the code
    print()
    print(timer)