scitex 2.0.0__py2.py3-none-any.whl → 2.1.0__py2.py3-none-any.whl

scitex/ml/plt/_plot_conf_mat.py

@@ -0,0 +1,663 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-10-02 07:15:10 (ywatanabe)"
+# File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/ml/plt/plot_conf_mat.py
+# ----------------------------------------
+from __future__ import annotations
+import os
+__FILE__ = __file__
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+
+import argparse
+
+import matplotlib
+import numpy as np
+import pandas as pd
+import scitex
+import seaborn as sns
+from matplotlib import ticker
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+from sklearn.metrics import balanced_accuracy_score
+from sklearn.metrics import confusion_matrix as sklearn_confusion_matrix
+
+# Import metric calculation from centralized location (SoC: metrics in scitex.ml.metrics)
+from scitex.ml.metrics import calc_bacc_from_conf_mat
+
+# Aliases for backward compatibility
+calc_bACC_from_conf_mat = calc_bacc_from_conf_mat
+
+
+def plot_conf_mat(
+    cm=None,
+    y_true=None,
+    y_pred=None,
+    y_pred_proba=None,
+    labels=None,
+    sorted_labels=None,
+    pred_labels=None,
+    sorted_pred_labels=None,
+    true_labels=None,
+    sorted_true_labels=None,
+    label_rotation_xy=(15, 15),
+    title="Confusion Matrix",
+    colorbar=True,
+    x_extend_ratio=1.0,
+    y_extend_ratio=1.0,
+    ax=None,
+    spath=None,
+):
+    """
+    Plot confusion matrix as a heatmap with inverted y-axis.
+
+    Parameters
+    ----------
+    cm : array-like, optional
+        Pre-computed confusion matrix
+    y_true : array-like, optional
+        True labels
+    y_pred : array-like, optional
+        Predicted labels
+    y_pred_proba : array-like, optional
+        Predicted probabilities
+    labels : list, optional
+        List of labels
+    sorted_labels : list, optional
+        Sorted list of labels
+    pred_labels : list, optional
+        Predicted label names
+    sorted_pred_labels : list, optional
+        Sorted predicted label names
+    true_labels : list, optional
+        True label names
+    sorted_true_labels : list, optional
+        Sorted true label names
+    label_rotation_xy : tuple, optional
+        Rotation angles for x and y labels
+    title : str, optional
+        Title of the plot
+    colorbar : bool, optional
+        Whether to include a colorbar
+    x_extend_ratio : float, optional
+        Ratio to extend x-axis
+    y_extend_ratio : float, optional
+        Ratio to extend y-axis
+    spath : str, optional
+        Path to save the figure
+    plt : deprecated
+        Kept for backward compatibility only
+    cm : array-like, optional
+        Pre-computed confusion matrix
+    y_true : array-like, optional
+        True labels
+    y_pred : array-like, optional
+        Predicted labels
+    y_pred_proba : array-like, optional
+        Predicted probabilities
+    labels : list, optional
+        List of labels
+    sorted_labels : list, optional
+        Sorted list of labels
+    pred_labels : list, optional
+        Predicted label names
+    sorted_pred_labels : list, optional
+        Sorted predicted label names
+    true_labels : list, optional
+        True label names
+    sorted_true_labels : list, optional
+        Sorted true label names
+    label_rotation_xy : tuple, optional
+        Rotation angles for x and y labels
+    title : str, optional
+        Title of the plot
+    colorbar : bool, optional
+        Whether to include a colorbar
+    x_extend_ratio : float, optional
+        Ratio to extend x-axis
+    y_extend_ratio : float, optional
+        Ratio to extend y-axis
+    spath : str, optional
+        Path to save the figure
+
+    Returns
+    -------
+    fig : matplotlib.figure.Figure
+        The figure object containing the plot
+    cm : pandas.DataFrame
+        The confusion matrix as a DataFrame
+
+    Example
+    -------
+    y_true = [0, 1, 2, 0, 1, 2]
+    y_pred = [0, 2, 1, 0, 0, 1]
+    labels = ['A', 'B', 'C']
+    fig, cm = conf_mat(plt, y_true=y_true, y_pred=y_pred, labels=labels)
+    plt.show()
+    """
+
+    if (y_pred_proba is not None) and (y_pred is None):
+        y_pred = y_pred_proba.argmax(axis=-1)
+
+    assert (cm is not None) or ((y_true is not None) and (y_pred is not None))
+
+    if cm is None:
+        with scitex.context.suppress_output():
+            cm = sklearn_confusion_matrix(y_true, y_pred, labels=labels)
+
+    bacc = calc_bACC_from_conf_mat(cm)
+
+    title = f"{title} (bACC = {bacc:.3f})"
+
+    # Only reconstruct full confusion matrix if we have y_true and y_pred
+    # When cm is passed directly, use it as-is
+    if labels is not None and y_true is not None and y_pred is not None:
+        full_cm = np.zeros((len(labels), len(labels)))
+        unique_true = np.unique(y_true)
+        unique_pred = np.unique(y_pred)
+        for idx_true, true_label in enumerate(labels):
+            for idx_pred, pred_label in enumerate(labels):
+                if true_label in unique_true and pred_label in unique_pred:
+                    full_cm[idx_true, idx_pred] = cm[
+                        np.where(unique_true == true_label)[0][0],
+                        np.where(unique_pred == pred_label)[0][0],
+                    ]
+        cm = full_cm
+
+    cm = pd.DataFrame(data=cm).copy()
+
+    labels_to_latex = lambda labels: (
+        [scitex.str.to_latex_style(label) for label in labels]
+        if labels is not None
+        else None
+    )
+    pred_labels = labels_to_latex(pred_labels)
+    true_labels = labels_to_latex(true_labels)
+    labels = labels_to_latex(labels)
+    sorted_labels = labels_to_latex(sorted_labels)
+
+    if pred_labels is not None:
+        cm.columns = pred_labels
+    elif labels is not None:
+        cm.columns = labels
+
+    if true_labels is not None:
+        cm.index = true_labels
+    elif labels is not None:
+        cm.index = labels
+
+    if sorted_labels is not None:
+        assert set(sorted_labels) == set(labels)
+        cm = cm.reindex(index=sorted_labels, columns=sorted_labels)
+
+    # Use stx.plt.subplots() for CSV export functionality
+    # The AxisWrapper provides export_as_csv method for automatic data export
+    import matplotlib.pyplot as mpl_plt
+    import scitex as stx
+
+    if ax is None:
+        fig, ax = stx.plt.subplots()
+    else:
+        fig = ax.get_figure()
+    res = sns.heatmap(
+        cm,
+        annot=True,
+        annot_kws={"size": mpl_plt.rcParams["font.size"]},
+        fmt=".0f",
+        cmap="Blues",
+        cbar=False,
+        vmin=0,
+    )
+
+    for text in ax.texts:
+        text.set_text("{:,d}".format(int(text.get_text())))
+
+    res.invert_yaxis()
+
+    for _, spine in res.spines.items():
+        spine.set_visible(False)
+
+    ax.set_xlabel("Predicted label")
+    ax.set_ylabel("True label")
+    ax.set_title(title)
+
+    ax = scitex.plt.ax.extend(ax, x_extend_ratio, y_extend_ratio)
+    if cm.shape[0] == cm.shape[1]:
+        ax.set_box_aspect(1)
+        ax.set_xticklabels(
+            ax.get_xticklabels(),
+            rotation=label_rotation_xy[0],
+            fontdict={"verticalalignment": "top"},
+        )
+        ax.set_yticklabels(
+            ax.get_yticklabels(),
+            rotation=label_rotation_xy[1],
+            fontdict={"horizontalalignment": "right"},
+        )
+
+    bbox = ax.get_position()
+    left_orig = bbox.x0
+    width_orig = bbox.x1 - bbox.x0
+    width_tgt = width_orig * x_extend_ratio
+    dx = width_orig - width_tgt
+
+    if colorbar:
+        # Extract underlying matplotlib axes if wrapped by SciTeX
+        ax_mpl = ax._axis_mpl if hasattr(ax, '_axis_mpl') else ax
+
+        divider = make_axes_locatable(ax_mpl)
+        cax = divider.append_axes("right", size="5%", pad=0.15)
+
+        # Get the underlying figure
+        fig_mpl = fig._fig_mpl if hasattr(fig, '_fig_mpl') else fig
+
+        vmax = np.array(cm).max().astype(int)
+        norm = matplotlib.colors.Normalize(vmin=0, vmax=vmax)
+        cbar = fig_mpl.colorbar(
+            matplotlib.cm.ScalarMappable(norm=norm, cmap="Blues"),
+            cax=cax,
+        )
+        cbar.locator = ticker.MaxNLocator(nbins=4)
+        cbar.update_ticks()
+        cbar.outline.set_edgecolor("white")
+
+    if spath is not None:
+        from pathlib import Path
+        # Resolve to absolute path to prevent _out directory creation
+        spath_abs = Path(spath).resolve() if isinstance(spath, (str, Path)) else spath
+        scitex.io.save(fig, str(spath_abs), use_caller_path=False)
+
+    return fig, cm
+
+
+# Backward compatibility alias
+conf_mat = plot_conf_mat
+
+
+# Metric calculation functions have been moved to scitex.ml.metrics
+# They are imported above for use in this module
+# This maintains SoC: plotting in scitex.ml.plt, metrics in scitex.ml.metrics
+
+
+def main(args):
+    """Demo confusion matrix plotting with Iris dataset."""
+    import sklearn
+    from sklearn import datasets, svm
+    from sklearn.model_selection import train_test_split
+
+    iris = datasets.load_iris()
+    X = iris.data
+    y = iris.target
+    class_names = iris.target_names
+
+    X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=42)
+
+    classifier = svm.SVC(kernel="linear", C=0.01, random_state=42).fit(
+        X_train, y_train
+    )
+
+    y_pred = classifier.predict(X_test)
+    cm_data = sklearn.metrics.confusion_matrix(y_test, y_pred)
+    cm_data **= 3
+
+    fig, cm_result = conf_mat(
+        cm=cm_data,
+        pred_labels=["A", "B", "C"],
+        true_labels=["a", "b", "c"],
+        label_rotation_xy=(60, 60),
+        x_extend_ratio=1.0,
+        colorbar=True,
+    )
+
+    fig.axes[-1] = scitex.plt.ax.sci_note(
+        fig.axes[-1],
+        fformat="%3.1f",
+        y=True,
+    )
+
+    scitex.io.save(fig, "plot_conf_mat_demo.jpg")
+    return 0
+
+
+def parse_args() -> argparse.Namespace:
+    """Parse command line arguments."""
+    import argparse
+    parser = argparse.ArgumentParser(description='Demo confusion matrix plotting')
+    return parser.parse_args()
+
+
+def run_main() -> None:
+    """Initialize scitex framework, run main function, and cleanup."""
+    global CONFIG, CC, sys, plt, rng
+
+    import sys
+    import matplotlib.pyplot as plt
+    import scitex as stx
+
+    args = parse_args()
+
+    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
+        sys,
+        plt,
+        args=args,
+        file=__FILE__,
+        sdir_suffix=None,
+        verbose=False,
+        agg=True,
+    )
+
+    exit_status = main(args)
+
+    stx.session.close(
+        CONFIG,
+        verbose=False,
+        notify=False,
+        message="",
+        exit_status=exit_status,
+    )
+
+
+if __name__ == "__main__":
+    run_main()
+
+# EOF
+
+# #!/usr/bin/env python3
+# import matplotlib
+# import scitex
+# import numpy as np
+# import pandas as pd
+# import seaborn as sns
+# from matplotlib import ticker
+# from mpl_toolkits.axes_grid1 import make_axes_locatable
+# from sklearn.metrics import balanced_accuracy_score
+# from sklearn.metrics import confusion_matrix as sklearn_confusion_matrix
+
+
+# def conf_mat(
+#     plt,
+#     cm=None,
+#     y_true=None,
+#     y_pred=None,
+#     y_pred_proba=None,
+#     labels=None,
+#     sorted_labels=None,
+#     pred_labels=None,
+#     sorted_pred_labels=None,
+#     true_labels=None,
+#     sorted_true_labels=None,
+#     label_rotation_xy=(15, 15),
+#     title="Confuxion Matrix",
+#     colorbar=True,
+#     x_extend_ratio=1.0,
+#     y_extend_ratio=1.0,
+#     spath=None,
+# ):
+#     """
+#     Inverse the y-axis and plot the confusion matrix as a heatmap.
+#     The predicted labels (in x-axis) is symboled with hat (^).
+#     The plt object is passed to adjust the figure size
+
+#     cm = sklearn.metrics.confusion_matrix(y_test, y_pred)
+
+
+#     cm = np.random.randint(low=0, high=10, size=[3,4])
+#     x: predicted labels
+#     y: true_labels
+
+
+#     kwargs:
+
+#         "extend_ratio":
+#             Determines how much the axes objects (not the fig object) are extended
+#             in the vertical direction.
+
+#     """
+
+#     if (y_pred_proba is not None) and (y_pred is None):
+#         y_pred = y_pred_proba.argmax(axis=-1)
+
+#     assert (cm is not None) or ((y_true is not None) and (y_pred is not None))
+
+#     if cm is None:
+#         with scitex.context.suppress_output():
+#             cm = sklearn_confusion_matrix(y_true, y_pred, labels=labels)
+#             # cm = sklearn_confusion_matrix(y_true, y_pred)
+
+#     bacc = calc_bACC_from_conf_mat(cm)
+
+#     title = f"{title} (bACC = {bacc})"
+
+#     # Ensure all labels are present in the confusion matrix
+#     if labels is not None:
+#         full_cm = np.zeros((len(labels), len(labels)))
+#         unique_true = np.unique(y_true)
+#         unique_pred = np.unique(y_pred)
+#         for i, true_label in enumerate(labels):
+#             for j, pred_label in enumerate(labels):
+#                 if true_label in unique_true and pred_label in unique_pred:
+#                     full_cm[i, j] = cm[
+#                         np.where(unique_true == true_label)[0][0],
+#                         np.where(unique_pred == pred_label)[0][0],
+#                     ]
+#         cm = full_cm
+
+#     # Dataframe
+#     cm = pd.DataFrame(
+#         data=cm,
+#     ).copy()
+
+#     # To LaTeX styles
+#     if pred_labels is not None:
+#         pred_labels = [scitex.str.to_latex_style(l) for l in pred_labels]
+#     if true_labels is not None:
+#         true_labels = [scitex.str.to_latex_style(l) for l in true_labels]
+#     if labels is not None:
+#         labels = [scitex.str.to_latex_style(l) for l in labels]
+#     if sorted_labels is not None:
+#         sorted_labels = [scitex.str.to_latex_style(l) for l in sorted_labels]
+
+#     # Prediction Labels: columns
+#     if pred_labels is not None:
+#         cm.columns = pred_labels
+#     elif (pred_labels is None) and (labels is not None):
+#         cm.columns = labels
+
+#     # Ground Truth Labels: index
+#     if true_labels is not None:
+#         cm.index = true_labels
+#     elif (true_labels is None) and (labels is not None):
+#         cm.index = labels
+
+#     # Sort based on sorted_labels here
+#     if sorted_labels is not None:
+#         assert set(sorted_labels) == set(labels)
+#         cm = cm.reindex(index=sorted_labels, columns=sorted_labels)
+
+#     # Main
+#     # Use stx.plt.subplots for advanced CSV export and SciTeX Viz integration
+    import matplotlib.pyplot as mpl_plt
+    import scitex as stx
+    fig, ax = stx.plt.subplots()
+#     res = sns.heatmap(
+#         cm,
+#         annot=True,
+#         annot_kws={"size": mpl_plt.rcParams["font.size"]},
+#         fmt=".0f",
+#         cmap="Blues",
+#         cbar=False,
+#         vmin=0,
+#     )  # Here, don't plot color bar.
+
+#     # Adds comma separator for the annotated int texts
+#     for t in ax.texts:
+#         t.set_text("{:,d}".format(int(t.get_text())))
+
+#     # Inverts the y-axis
+#     res.invert_yaxis()
+
+#     # Makes the frame visible
+#     for _, spine in res.spines.items():
+#         spine.set_visible(False)
+
+#     # Labels
+#     ax.set_xlabel("Predicted label")
+#     ax.set_ylabel("True label")
+#     ax.set_title(title)
+
+#     # Appearances
+#     ax = scitex.plt.ax.extend(ax, x_extend_ratio, y_extend_ratio)
+#     if cm.shape[0] == cm.shape[1]:
+#         ax.set_box_aspect(1)
+#         ax.set_xticklabels(
+#             ax.get_xticklabels(),
+#             rotation=label_rotation_xy[0],
+#             fontdict={"verticalalignment": "top"},
+#         )
+#         ax.set_yticklabels(
+#             ax.get_yticklabels(),
+#             rotation=label_rotation_xy[1],
+#             fontdict={"horizontalalignment": "right"},
+#         )
+#         # The size
+#     bbox = ax.get_position()
+#     left_orig = bbox.x0
+#     width_orig = bbox.x1 - bbox.x0
+#     g_x_orig = left_orig + width_orig / 2.0
+#     width_tgt = width_orig * x_extend_ratio  # x_extend_ratio
+#     dx = width_orig - width_tgt
+
+#     # Adjusts the sizes of the confusion matrix and colorbar
+#     if colorbar:
+#         divider = make_axes_locatable(ax)  # Gets region from the ax
+#         cax = divider.append_axes("right", size="5%", pad=0.1)
+#         # cax = divider.new_horizontal(size="5%", pad=1, pack_start=True)
+#         cax = scitex.plt.ax.shift(cax, dx=-dx * 2.54, dy=0)
+#         fig.add_axes(cax)
+
+#         """
+#         axpos = ax.get_position()
+#         caxpos = cax.get_position()
+
+#         AddAxesBBoxRect(fig, ax, ec="r")
+#         AddAxesBBoxRect(fig, cax, ec="b")
+
+#         fig.text(
+#             axpos.x0 + 0.01, axpos.y0 + 0.01, "after colorbar", weight="bold", color="r"
+#         )
+
+#         fig.text(
+#             caxpos.x1 + 0.01,
+#             caxpos.y1 - 0.01,
+#             "cax position",
+#             va="top",
+#             weight="bold",
+#             color="b",
+#             rotation="vertical",
+#         )
+#         """
+
+#         # Plots colorbar and adjusts the size
+#         vmax = np.array(cm).max().astype(int)
+#         norm = matplotlib.colors.Normalize(vmin=0, vmax=vmax)
+#         cbar = fig.colorbar(
+#             plt.cm.ScalarMappable(norm=norm, cmap="Blues"),
+#             cax=cax,
+#             # shrink=0.68,
+#         )
+#         cbar.locator = ticker.MaxNLocator(nbins=4)  # tick_locator
+#         cbar.update_ticks()
+#         # cbar.outline.set_edgecolor("#f9f2d7")
+#         cbar.outline.set_edgecolor("white")
+
+#     if spath is not None:
+#         scitex.io.save(fig, spath)
+
+#     return fig, cm
+
+
+# def calc_bACC_from_conf_mat(cm):
+#     with scitex.context.suppress_output():
+#         try:
+#             per_class = np.diag(cm) / np.nansum(cm, axis=1)
+#             bacc = round(np.nanmean(per_class), 3)
+#         except:
+#             bacc = np.nan
+#         return bacc
+
+
+# # def AddAxesBBoxRect(fig, ax, ec="k"):
+# #     from matplotlib.patches import Rectangle
+
+# #     axpos = ax.get_position()
+# #     rect = fig.patches.append(
+# #         Rectangle(
+# #             (axpos.x0, axpos.y0),
+# #             axpos.width,
+# #             axpos.height,
+# #             ls="solid",
+# #             lw=2,
+# #             ec=ec,
+# #             fill=False,
+# #             transform=fig.transFigure,
+# #         )
+# #     )
+# #     return rect
+
+
+# if __name__ == "__main__":
+
+#     import sys
+
+#     import matplotlib.pyplot as plt
+#     import scitex
+#     import numpy as np
+#     import sklearn
+#     from sklearn import datasets, svm
+#     # from sklearn.metrics import plot_confusion_matrix
+#     from sklearn.model_selection import train_test_split
+
+#     sys.path.append(".")
+#     import scitex
+
+#     # https://scikit-learn.org/stable/auto_examples/model_selection/plot_confusion_matrix.html#sphx-glr-auto-examples-model-selection-plot-confusion-matrix-py
+#     # Imports some data to play with
+#     iris = datasets.load_iris()
+#     X = iris.data
+#     y = iris.target
+#     class_names = iris.target_names
+
+#     # Splits the data into a training set and a test set
+#     X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
+
+#     # Runs classifier, using a model that is too regularized (C too low) to see
+#     # the impact on the results
+#     classifier = svm.SVC(kernel="linear", C=0.01).fit(X_train, y_train)
+
+#     ## Checks the confusion_matrix function
+#     y_pred = classifier.predict(X_test)
+#     cm = sklearn.metrics.confusion_matrix(y_test, y_pred)
+#     cm **= 3
+
+#     fig, cm = conf_mat(
+#         plt,
+#         # y_true=y_test,
+#         # y_pred=y_pred,
+#         cm,
+#         pred_labels=["A", "B", "C"],
+#         true_labels=["a", "b", "c"],
+#         label_rotation_xy=(60, 60),
+#         x_extend_ratio=1.0,
+#         colorbar=True,
+#     )
+
+#     fig.axes[-1] = scitex.plt.ax.sci_note(
+#         fig.axes[-1],
+#         fformat="%3.1f",
+#         y=True,
+#     )
+
+#     plt.show()
+
+#     ## EOF
+
+# EOF