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The function `calculate_kmeans` performs KMeans clustering on PCA embeddings data to assign
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labels and centroids.
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:param pca_embeddings: The `pca_embeddings` parameter is a NumPy array containing the data points.
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:param num_classes: The `num_classes` parameter is an integer that specifies the number of clusters.
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:param iter: The `iter` parameter is an integer that specifies the number of iterations for the KMeans algorithm. Default is 10. Should be a positive integer.
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