lab5

.idea/.gitignore

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+# Default ignored files
+/shelf/
+/workspace.xml
+# Editor-based HTTP Client requests
+/httpRequests/
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml

.idea/MII.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/venv" />
+    </content>
+    <orderEntry type="jdk" jdkName="Python 3.12 (2)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>

.idea/inspectionProfiles/profiles_settings.xml

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+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

.idea/misc.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Black">
+    <option name="sdkName" value="Python 3.12 (2)" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.12 (2)" project-jdk-type="Python SDK" />
+</project>

.idea/modules.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/MII.iml" filepath="$PROJECT_DIR$/.idea/MII.iml" />
+    </modules>
+  </component>
+</project>

.idea/vcs.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>

mai/utils_clusters.py

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+import math
+from typing import Dict, List, Tuple
+
+import numpy as np
+from pandas import DataFrame
+from sklearn import cluster
+from sklearn.metrics import silhouette_samples, silhouette_score
+
+
+def run_agglomerative(
+    df: DataFrame, num_clusters: int | None = 2
+) -> cluster.AgglomerativeClustering:
+    agglomerative = cluster.AgglomerativeClustering(
+        n_clusters=num_clusters,
+        compute_distances=True,
+    )
+    return agglomerative.fit(df)
+
+
+def get_linkage_matrix(model: cluster.AgglomerativeClustering) -> np.ndarray:
+    counts = np.zeros(model.children_.shape[0])  # type: ignore
+    n_samples = len(model.labels_)
+    for i, merge in enumerate(model.children_):  # type: ignore
+        current_count = 0
+        for child_idx in merge:
+            if child_idx < n_samples:
+                current_count += 1
+            else:
+                current_count += counts[child_idx - n_samples]
+        counts[i] = current_count
+
+    return np.column_stack([model.children_, model.distances_, counts]).astype(float)
+
+
+def print_cluster_result(
+    df: DataFrame, clusters_num: int, labels: np.ndarray, separator: str = ", "
+):
+    for cluster_id in range(clusters_num):
+        cluster_indices = np.where(labels == cluster_id)[0]
+        print(f"Cluster {cluster_id + 1} ({len(cluster_indices)}):")
+        rules = [str(df.index[idx]) for idx in cluster_indices]
+        print(separator.join(rules))
+        print("")
+        print("--------")
+
+
+def run_kmeans(
+    df: DataFrame, num_clusters: int, random_state: int
+) -> Tuple[np.ndarray, np.ndarray]:
+    kmeans = cluster.KMeans(n_clusters=num_clusters, random_state=random_state)
+    labels = kmeans.fit_predict(df)
+    return labels, kmeans.cluster_centers_
+
+
+def fit_kmeans(
+    reduced_data: np.ndarray, num_clusters: int, random_state: int
+) -> cluster.KMeans:
+    kmeans = cluster.KMeans(n_clusters=num_clusters, random_state=random_state)
+    kmeans.fit(reduced_data)
+    return kmeans
+
+
+def _get_kmeans_range(
+    df: DataFrame | np.ndarray, random_state: int
+) -> Tuple[List, range]:
+    max_clusters = int(math.sqrt(len(df)))
+    clusters_range = range(2, max_clusters + 1)
+    kmeans_per_k = [
+        cluster.KMeans(n_clusters=k, random_state=random_state).fit(df)
+        for k in clusters_range
+    ]
+    return kmeans_per_k, clusters_range
+
+
+def get_clusters_inertia(df: DataFrame, random_state: int) -> Tuple[List, range]:
+    kmeans_per_k, clusters_range = _get_kmeans_range(df, random_state)
+    return [model.inertia_ for model in kmeans_per_k], clusters_range
+
+
+def get_clusters_silhouette_scores(
+    df: DataFrame, random_state: int
+) -> Tuple[List, range]:
+    kmeans_per_k, clusters_range = _get_kmeans_range(df, random_state)
+    return [
+        float(silhouette_score(df, model.labels_)) for model in kmeans_per_k
+    ], clusters_range
+
+
+def get_clusters_silhouettes(df: np.ndarray, random_state: int) -> Dict:
+    kmeans_per_k, _ = _get_kmeans_range(df, random_state)
+    clusters_silhouettes: Dict = {}
+    for model in kmeans_per_k:
+        silhouette_value = silhouette_score(df, model.labels_)
+        sample_silhouette_values = silhouette_samples(df, model.labels_)
+        clusters_silhouettes[model.n_clusters] = (
+            silhouette_value,
+            sample_silhouette_values,
+            model,
+        )
+    return clusters_silhouettes

mai/visual.py

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+from typing import Any, Dict, List
+
+import matplotlib.cm as cm
+import matplotlib.pyplot as plt
+import numpy as np
+from pandas import DataFrame
+from scipy.cluster import hierarchy
+from sklearn.cluster import KMeans
+
+
+def draw_data_2d(
+    df: DataFrame,
+    col1: int,
+    col2: int,
+    y: List | None = None,
+    classes: List | None = None,
+    subplot: Any | None = None,
+):
+    ax = None
+    if subplot is None:
+        _, ax = plt.subplots()
+    else:
+        ax = subplot
+    scatter = ax.scatter(df[df.columns[col1]], df[df.columns[col2]], c=y)
+    ax.set(xlabel=df.columns[col1], ylabel=df.columns[col2])
+    if classes is not None:
+        ax.legend(
+            scatter.legend_elements()[0], classes, loc="lower right", title="Classes"
+        )
+
+
+def draw_dendrogram(linkage_matrix: np.ndarray):
+    hierarchy.dendrogram(linkage_matrix, truncate_mode="level", p=3)
+
+
+def draw_cluster_results(
+    df: DataFrame,
+    col1: int,
+    col2: int,
+    labels: np.ndarray,
+    cluster_centers: np.ndarray,
+    subplot: Any | None = None,
+):
+    ax = None
+    if subplot is None:
+        ax = plt
+    else:
+        ax = subplot
+
+    centroids = cluster_centers
+    u_labels = np.unique(labels)
+
+    for i in u_labels:
+        ax.scatter(
+            df[labels == i][df.columns[col1]],
+            df[labels == i][df.columns[col2]],
+            label=i,
+        )
+
+    ax.scatter(centroids[:, col1], centroids[:, col2], s=80, color="k")
+
+
+def draw_clusters(reduced_data: np.ndarray, kmeans: KMeans):
+    h = 0.02
+
+    x_min, x_max = reduced_data[:, 0].min() - 1, reduced_data[:, 0].max() + 1
+    y_min, y_max = reduced_data[:, 1].min() - 1, reduced_data[:, 1].max() + 1
+    xx, yy = np.meshgrid(np.arange(x_min, x_max, h), np.arange(y_min, y_max, h))
+
+    Z = kmeans.predict(np.c_[xx.ravel(), yy.ravel()])
+
+    Z = Z.reshape(xx.shape)
+    plt.figure(1)
+    plt.clf()
+    plt.imshow(
+        Z,
+        interpolation="nearest",
+        extent=(xx.min(), xx.max(), yy.min(), yy.max()),
+        cmap=plt.cm.Paired,  # type: ignore
+        aspect="auto",
+        origin="lower",
+    )
+
+    plt.plot(reduced_data[:, 0], reduced_data[:, 1], "k.", markersize=2)
+    centroids = kmeans.cluster_centers_
+    plt.scatter(
+        centroids[:, 0],
+        centroids[:, 1],
+        marker="x",
+        s=169,
+        linewidths=3,
+        color="w",
+        zorder=10,
+    )
+    plt.title(
+        "K-means clustering (PCA-reduced data)\n"
+        "Centroids are marked with white cross"
+    )
+    plt.xlim(x_min, x_max)
+    plt.ylim(y_min, y_max)
+    plt.xticks(())
+    plt.yticks(())
+
+
+def _draw_cluster_scores(
+    data: List,
+    clusters_range: range,
+    score_name: str,
+    title: str,
+):
+    plt.figure(figsize=(8, 5))
+    plt.plot(clusters_range, data, "bo-")
+    plt.xlabel("$k$", fontsize=8)
+    plt.ylabel(score_name, fontsize=8)
+    plt.title(title)
+
+
+def draw_elbow_diagram(inertias: List, clusters_range: range):
+    _draw_cluster_scores(inertias, clusters_range, "Inertia", "The Elbow Diagram")
+
+
+def draw_silhouettes_diagram(silhouette: List, clusters_range: range):
+    _draw_cluster_scores(
+        silhouette, clusters_range, "Silhouette score", "The Silhouette score"
+    )
+
+
+def _draw_silhouette(
+    ax: Any,
+    reduced_data: np.ndarray,
+    n_clusters: int,
+    silhouette_avg: float,
+    sample_silhouette_values: List,
+    cluster_labels: List,
+):
+    ax.set_xlim([-0.1, 1])
+    ax.set_ylim([0, len(reduced_data) + (n_clusters + 1) * 10])
+
+    y_lower = 10
+    for i in range(n_clusters):
+        ith_cluster_silhouette_values = sample_silhouette_values[cluster_labels == i]
+
+        ith_cluster_silhouette_values.sort()
+
+        size_cluster_i = ith_cluster_silhouette_values.shape[0]
+        y_upper = y_lower + size_cluster_i
+
+        color = cm.nipy_spectral(float(i) / n_clusters)  # type: ignore
+        ax.fill_betweenx(
+            np.arange(y_lower, y_upper),
+            0,
+            ith_cluster_silhouette_values,
+            facecolor=color,
+            edgecolor=color,
+            alpha=0.7,
+        )
+
+        ax.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
+
+        y_lower = y_upper + 10  # 10 for the 0 samples
+
+    ax.set_title("The silhouette plot for the various clusters.")
+    ax.set_xlabel("The silhouette coefficient values")
+    ax.set_ylabel("Cluster label")
+
+    ax.axvline(x=silhouette_avg, color="red", linestyle="--")
+
+    ax.set_yticks([])
+    ax.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
+
+
+def _draw_cluster_data(
+    ax: Any,
+    reduced_data: np.ndarray,
+    n_clusters: int,
+    cluster_labels: np.ndarray,
+    cluster_centers: np.ndarray,
+):
+    colors = cm.nipy_spectral(cluster_labels.astype(float) / n_clusters)  # type: ignore
+    ax.scatter(
+        reduced_data[:, 0],
+        reduced_data[:, 1],
+        marker=".",
+        s=30,
+        lw=0,
+        alpha=0.7,
+        c=colors,
+        edgecolor="k",
+    )
+
+    ax.scatter(
+        cluster_centers[:, 0],
+        cluster_centers[:, 1],
+        marker="o",
+        c="white",
+        alpha=1,
+        s=200,
+        edgecolor="k",
+    )
+
+    for i, c in enumerate(cluster_centers):
+        ax.scatter(c[0], c[1], marker="$%d$" % i, alpha=1, s=50, edgecolor="k")
+
+    ax.set_title("The visualization of the clustered data.")
+    ax.set_xlabel("Feature space for the 1st feature")
+    ax.set_ylabel("Feature space for the 2nd feature")
+
+
+def draw_silhouettes(reduced_data: np.ndarray, silhouettes: Dict):
+    for key, value in silhouettes.items():
+        fig, (ax1, ax2) = plt.subplots(1, 2)
+        fig.set_size_inches(18, 7)
+
+        n_clusters = key
+        silhouette_avg = value[0]
+        sample_silhouette_values = value[1]
+        cluster_labels = value[2].labels_
+        cluster_centers = value[2].cluster_centers_
+
+        _draw_silhouette(
+            ax1,
+            reduced_data,
+            n_clusters,
+            silhouette_avg,
+            sample_silhouette_values,
+            cluster_labels,
+        )
+
+        _draw_cluster_data(
+            ax2,
+            reduced_data,
+            n_clusters,
+            cluster_labels,
+            cluster_centers,
+        )
+
+        plt.suptitle(
+            "Silhouette analysis for KMeans clustering on sample data with n_clusters = %d"
+            % n_clusters,
+            fontsize=14,
+            fontweight="bold",
+        )