scitex 2.7.0__py3-none-any.whl → 2.7.3__py3-none-any.whl

scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/__init__.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-12-13 (ywatanabe)"
+# File: __init__.py - MatplotlibPlotMixin package
+
+"""
+MatplotlibPlotMixin - Modular plotting mixin for AxisWrapper.
+
+This package provides plotting functionality split into logical submodules:
+- _base: Core helper methods
+- _scientific: Scientific/specialized plots (stx_image, stx_kde, stx_conf_mat, etc.)
+- _statistical: Statistical plots (stx_line, stx_mean_std, stx_box, stx_violin, hist)
+- _stx_aliases: stx_ prefixed aliases for standard matplotlib methods
+
+API Layer Design:
+-----------------
+stx_* (SciTeX canonical):
+  - Full tracking, metadata, and reproducibility support
+  - Output connects to .pltz / .figz format
+  - Purpose: publication / reproducibility
+
+mpl_* (Matplotlib compatibility - see _RawMatplotlibMixin):
+  - Raw matplotlib API without scitex processing
+  - Purpose: compatibility / low-level control / escape hatch
+
+sns_* (Seaborn - see _SeabornMixin):
+  - DataFrame-centric with data=, x=, y=, hue= interface
+  - Purpose: exploratory / grouped stats
+"""
+
+import os
+
+__FILE__ = __file__
+__DIR__ = os.path.dirname(__FILE__)
+
+from ._base import PlotBaseMixin
+from ._scientific import ScientificPlotMixin
+from ._statistical import StatisticalPlotMixin
+from ._stx_aliases import StxAliasesMixin
+
+
+class MatplotlibPlotMixin(
+    PlotBaseMixin,
+    ScientificPlotMixin,
+    StatisticalPlotMixin,
+    StxAliasesMixin,
+):
+    """Mixin class for basic plotting operations.
+
+    Combines multiple specialized mixins:
+    - PlotBaseMixin: Core helper methods (_get_ax_module, _apply_scitex_postprocess)
+    - ScientificPlotMixin: Scientific plots (stx_image, stx_kde, stx_conf_mat, etc.)
+    - StatisticalPlotMixin: Statistical line plots and distributions
+    - StxAliasesMixin: stx_ prefixed matplotlib aliases
+    """
+    pass
+
+
+# EOF

scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_base.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-12-13 (ywatanabe)"
+# File: _base.py - Core helper methods for MatplotlibPlotMixin
+
+"""Base mixin with core helper methods for plotting."""
+
+import os
+
+__FILE__ = __file__
+__DIR__ = os.path.dirname(__FILE__)
+
+
+class PlotBaseMixin:
+    """Base mixin with core helper methods for plotting."""
+
+    def _get_ax_module(self):
+        """Lazy import ax module to avoid circular imports."""
+        from .....plt import ax as ax_module
+        return ax_module
+
+    def _apply_scitex_postprocess(
+        self, method_name, result=None, kwargs=None, args=None
+    ):
+        """Apply scitex post-processing styling after plotting.
+
+        This ensures all scitex wrapper methods get the same styling
+        as matplotlib methods going through __getattr__ (tick locator, spines, etc.).
+        """
+        from scitex.plt.styles import apply_plot_postprocess
+        apply_plot_postprocess(method_name, result, self._axis_mpl, kwargs or {}, args)
+
+
+# EOF

scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_scientific.py

@@ -0,0 +1,593 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-12-13 (ywatanabe)"
+# File: _scientific.py - Scientific/specialized plot methods
+
+"""Scientific and domain-specific plotting methods."""
+
+import os
+from typing import Any, Dict, List, Optional, Tuple
+
+import matplotlib
+import numpy as np
+import pandas as pd
+from scipy.stats import gaussian_kde
+
+from scitex.pd import to_xyz
+from scitex.types import ArrayLike
+
+__FILE__ = __file__
+__DIR__ = os.path.dirname(__FILE__)
+
+
+class ScientificPlotMixin:
+    """Mixin for scientific and domain-specific plotting methods.
+
+    Provides specialized visualizations for:
+    - Image display with colorbars
+    - Kernel density estimation
+    - Confusion matrices
+    - Raster plots (spike trains)
+    - ECDF plots
+    - Joint distributions (scatter + marginal histograms)
+    - Heatmaps with annotations
+    """
+
+    def stx_image(
+        self,
+        data: ArrayLike,
+        *,
+        track: bool = True,
+        id: Optional[str] = None,
+        **kwargs,
+    ) -> "Axes":
+        """Display a 2D array as an image with SciTeX styling.
+
+        Parameters
+        ----------
+        data : array-like
+            2D array to display as an image.
+        track : bool, default True
+            Enable data tracking for reproducibility.
+        id : str, optional
+            Unique identifier for this plot element.
+        **kwargs
+            Additional arguments passed to the image function.
+            Common options: cmap, vmin, vmax, aspect, colorbar.
+
+        Returns
+        -------
+        Axes
+            The axes with the image displayed.
+
+        See Also
+        --------
+        stx_imshow : Lower-level image display.
+        stx_heatmap : Annotated heatmap.
+        sns_heatmap : DataFrame-based heatmap.
+
+        Examples
+        --------
+        >>> ax.stx_image(matrix, cmap='viridis', colorbar=True)
+        """
+        method_name = "stx_image"
+
+        with self._no_tracking():
+            self._axis_mpl = self._get_ax_module().stx_image(
+                self._axis_mpl, data, **kwargs
+            )
+
+        tracked_dict = {"image_df": pd.DataFrame(data)}
+        if kwargs.get("xyz", False):
+            tracked_dict["image_df"] = to_xyz(tracked_dict["image_df"])
+        self._track(track, id, method_name, tracked_dict, None)
+        self._apply_scitex_postprocess(method_name)
+
+        return self._axis_mpl
+
+    def stx_kde(
+        self,
+        data: ArrayLike,
+        *,
+        cumulative: bool = False,
+        fill: bool = False,
+        xlim: Optional[Tuple[float, float]] = None,
+        track: bool = True,
+        id: Optional[str] = None,
+        **kwargs,
+    ) -> "Axes":
+        """Plot a kernel density estimate of the data.
+
+        Parameters
+        ----------
+        data : array-like
+            1D array of values for density estimation.
+        cumulative : bool, default False
+            If True, plot cumulative distribution instead of density.
+        fill : bool, default False
+            If True, fill the area under the curve.
+        xlim : tuple of float, optional
+            Range for the x-axis. If None, uses data range.
+        track : bool, default True
+            Enable data tracking for reproducibility.
+        id : str, optional
+            Unique identifier for this plot element.
+        **kwargs
+            Additional arguments passed to the plot function.
+            Common options: color, linewidth, linestyle, label.
+
+        Returns
+        -------
+        Axes
+            The axes with the KDE plot.
+
+        See Also
+        --------
+        sns_kdeplot : DataFrame-based KDE plot.
+        stx_ecdf : Empirical cumulative distribution function.
+        hist : Histogram alternative.
+
+        Examples
+        --------
+        >>> ax.stx_kde(samples, fill=True, alpha=0.3)
+        >>> ax.stx_kde(data, cumulative=True, label='CDF')
+        """
+        method_name = "stx_kde"
+
+        n_samples = (~np.isnan(data)).sum()
+        if kwargs.get("label"):
+            kwargs["label"] = f"{kwargs['label']} ($n$={n_samples})"
+
+        if xlim is None:
+            xlim = (np.nanmin(data), np.nanmax(data))
+
+        xx = np.linspace(xlim[0], xlim[1], int(1e3))
+        density = gaussian_kde(data)(xx)
+        density /= density.sum()
+
+        if cumulative:
+            density = np.cumsum(density)
+
+        with self._no_tracking():
+            from scitex.plt.utils import mm_to_pt
+
+            if "linewidth" not in kwargs and "lw" not in kwargs:
+                kwargs["linewidth"] = mm_to_pt(0.2)
+            if "color" not in kwargs and "c" not in kwargs:
+                kwargs["color"] = "black"
+            if "linestyle" not in kwargs and "ls" not in kwargs:
+                kwargs["linestyle"] = "--"
+
+            if fill:
+                self._axis_mpl.fill_between(xx, density, **kwargs)
+            else:
+                self._axis_mpl.plot(xx, density, **kwargs)
+
+        tracked_dict = {"x": xx, "kde": density, "n": n_samples}
+        self._track(track, id, method_name, tracked_dict, None)
+        self._apply_scitex_postprocess(method_name)
+
+        return self._axis_mpl
+
+    def stx_conf_mat(
+        self,
+        data: ArrayLike,
+        *,
+        x_labels: Optional[List[str]] = None,
+        y_labels: Optional[List[str]] = None,
+        title: str = "Confusion Matrix",
+        cmap: str = "Blues",
+        cbar: bool = True,
+        cbar_kw: Optional[Dict[str, Any]] = None,
+        label_rotation_xy: Tuple[float, float] = (15, 15),
+        x_extend_ratio: float = 1.0,
+        y_extend_ratio: float = 1.0,
+        calc_bacc: bool = False,
+        track: bool = True,
+        id: Optional[str] = None,
+        **kwargs,
+    ) -> Tuple["Axes", Optional[float]]:
+        """Plot a confusion matrix with optional balanced accuracy calculation.
+
+        Parameters
+        ----------
+        data : array-like
+            2D confusion matrix array.
+        x_labels : list of str, optional
+            Labels for x-axis (predicted classes).
+        y_labels : list of str, optional
+            Labels for y-axis (true classes).
+        title : str, default 'Confusion Matrix'
+            Title for the plot.
+        cmap : str, default 'Blues'
+            Colormap for the heatmap.
+        cbar : bool, default True
+            Whether to show the colorbar.
+        cbar_kw : dict, optional
+            Additional keyword arguments for the colorbar.
+        label_rotation_xy : tuple of float, default (15, 15)
+            Rotation angles for (x, y) axis labels.
+        x_extend_ratio : float, default 1.0
+            Ratio to extend x-axis limits.
+        y_extend_ratio : float, default 1.0
+            Ratio to extend y-axis limits.
+        calc_bacc : bool, default False
+            Whether to calculate and return balanced accuracy.
+        track : bool, default True
+            Enable data tracking for reproducibility.
+        id : str, optional
+            Unique identifier for this plot element.
+        **kwargs
+            Additional arguments passed to the heatmap function.
+
+        Returns
+        -------
+        tuple
+            (Axes, balanced_accuracy) - balanced_accuracy is None if calc_bacc=False.
+
+        Examples
+        --------
+        >>> ax.stx_conf_mat(cm, x_labels=['A', 'B'], y_labels=['A', 'B'])
+        >>> ax, bacc = ax.stx_conf_mat(cm, calc_bacc=True)
+        """
+        method_name = "stx_conf_mat"
+
+        if cbar_kw is None:
+            cbar_kw = {}
+
+        with self._no_tracking():
+            self._axis_mpl, bacc_val = self._get_ax_module().stx_conf_mat(
+                self._axis_mpl,
+                data,
+                x_labels=x_labels,
+                y_labels=y_labels,
+                title=title,
+                cmap=cmap,
+                cbar=cbar,
+                cbar_kw=cbar_kw,
+                label_rotation_xy=label_rotation_xy,
+                x_extend_ratio=x_extend_ratio,
+                y_extend_ratio=y_extend_ratio,
+                calc_bacc=calc_bacc,
+                **kwargs,
+            )
+
+        tracked_dict = {
+            "args": [data],
+            "balanced_accuracy": bacc_val,
+            "x_labels": x_labels,
+            "y_labels": y_labels,
+        }
+        self._track(track, id, method_name, tracked_dict, None)
+        self._apply_scitex_postprocess(method_name)
+
+        return self._axis_mpl, bacc_val
+
+    def stx_raster(
+        self,
+        spike_times: List[ArrayLike],
+        *,
+        time: Optional[ArrayLike] = None,
+        labels: Optional[List[str]] = None,
+        colors: Optional[List[str]] = None,
+        track: bool = True,
+        id: Optional[str] = None,
+        **kwargs,
+    ) -> Tuple["Axes", pd.DataFrame]:
+        """Plot a raster plot (spike train visualization).
+
+        Parameters
+        ----------
+        spike_times : list of array-like
+            List of arrays, each containing spike times for one unit/neuron.
+        time : array-like, optional
+            Time axis reference. If None, uses spike time range.
+        labels : list of str, optional
+            Labels for each unit/row.
+        colors : list of str, optional
+            Colors for each unit/row.
+        track : bool, default True
+            Enable data tracking for reproducibility.
+        id : str, optional
+            Unique identifier for this plot element.
+        **kwargs
+            Additional arguments passed to the raster function.
+
+        Returns
+        -------
+        tuple
+            (Axes, DataFrame) - The axes and digitized raster data.
+
+        Examples
+        --------
+        >>> ax.stx_raster([spikes_unit1, spikes_unit2], labels=['Unit 1', 'Unit 2'])
+        """
+        method_name = "stx_raster"
+
+        with self._no_tracking():
+            self._axis_mpl, raster_digit_df = self._get_ax_module().stx_raster(
+                self._axis_mpl, spike_times, time=time
+            )
+
+        tracked_dict = {"raster_digit_df": raster_digit_df}
+        self._track(track, id, method_name, tracked_dict, None)
+        self._apply_scitex_postprocess(method_name)
+
+        return self._axis_mpl, raster_digit_df
+
+    def stx_ecdf(
+        self,
+        data: ArrayLike,
+        *,
+        track: bool = True,
+        id: Optional[str] = None,
+        **kwargs,
+    ) -> Tuple["Axes", pd.DataFrame]:
+        """Plot an empirical cumulative distribution function (ECDF).
+
+        Parameters
+        ----------
+        data : array-like
+            1D array of values.
+        track : bool, default True
+            Enable data tracking for reproducibility.
+        id : str, optional
+            Unique identifier for this plot element.
+        **kwargs
+            Additional arguments passed to the ECDF function.
+            Common options: color, linewidth, label.
+
+        Returns
+        -------
+        tuple
+            (Axes, DataFrame) - The axes and ECDF data (x, y columns).
+
+        See Also
+        --------
+        stx_kde : Kernel density estimate (continuous).
+        hist : Histogram (discrete bins).
+
+        Examples
+        --------
+        >>> ax.stx_ecdf(samples, label='Distribution A')
+        """
+        method_name = "stx_ecdf"
+
+        with self._no_tracking():
+            self._axis_mpl, ecdf_df = self._get_ax_module().stx_ecdf(
+                self._axis_mpl, data, **kwargs
+            )
+
+        tracked_dict = {"ecdf_df": ecdf_df}
+        self._track(track, id, method_name, tracked_dict, None)
+        self._apply_scitex_postprocess(method_name)
+
+        return self._axis_mpl, ecdf_df
+
+    def stx_joyplot(
+        self,
+        data: ArrayLike,
+        *,
+        track: bool = True,
+        id: Optional[str] = None,
+        **kwargs,
+    ) -> "Axes":
+        """Plot a joyplot (ridgeline plot) for distribution comparison.
+
+        Parameters
+        ----------
+        data : array-like
+            2D array where each row is a distribution to plot.
+        track : bool, default True
+            Enable data tracking for reproducibility.
+        id : str, optional
+            Unique identifier for this plot element.
+        **kwargs
+            Additional arguments passed to the joyplot function.
+
+        Returns
+        -------
+        Axes
+            The axes with the joyplot.
+
+        Examples
+        --------
+        >>> ax.stx_joyplot(distributions_2d, overlap=0.5)
+        """
+        method_name = "stx_joyplot"
+
+        with self._no_tracking():
+            self._axis_mpl = self._get_ax_module().stx_joyplot(
+                self._axis_mpl, data, **kwargs
+            )
+
+        tracked_dict = {"joyplot_data": data}
+        self._track(track, id, method_name, tracked_dict, None)
+        self._apply_scitex_postprocess(method_name)
+
+        return self._axis_mpl
+
+    def stx_scatter_hist(
+        self,
+        x: ArrayLike,
+        y: ArrayLike,
+        *,
+        hist_bins: int = 20,
+        scatter_alpha: float = 0.6,
+        scatter_size: float = 20,
+        scatter_color: str = "blue",
+        hist_color_x: str = "blue",
+        hist_color_y: str = "red",
+        hist_alpha: float = 0.5,
+        scatter_ratio: float = 0.8,
+        track: bool = True,
+        id: Optional[str] = None,
+        **kwargs,
+    ) -> Tuple["Axes", "Axes", "Axes", Dict]:
+        """Plot a scatter plot with marginal histograms.
+
+        Parameters
+        ----------
+        x : array-like
+            X coordinates of the scatter points.
+        y : array-like
+            Y coordinates of the scatter points.
+        hist_bins : int, default 20
+            Number of bins for the marginal histograms.
+        scatter_alpha : float, default 0.6
+            Transparency of scatter points.
+        scatter_size : float, default 20
+            Size of scatter points.
+        scatter_color : str, default 'blue'
+            Color of scatter points.
+        hist_color_x : str, default 'blue'
+            Color of x-marginal histogram.
+        hist_color_y : str, default 'red'
+            Color of y-marginal histogram.
+        hist_alpha : float, default 0.5
+            Transparency of histograms.
+        scatter_ratio : float, default 0.8
+            Ratio of scatter plot area to total area.
+        track : bool, default True
+            Enable data tracking for reproducibility.
+        id : str, optional
+            Unique identifier for this plot element.
+        **kwargs
+            Additional arguments passed to the scatter function.
+
+        Returns
+        -------
+        tuple
+            (main_ax, hist_x_ax, hist_y_ax, hist_data) - Axes and histogram data.
+
+        See Also
+        --------
+        stx_scatter : Simple scatter plot.
+        sns_jointplot : Seaborn joint plot.
+
+        Examples
+        --------
+        >>> ax, ax_hx, ax_hy, data = ax.stx_scatter_hist(x, y, hist_bins=30)
+        """
+        method_name = "stx_scatter_hist"
+
+        with self._no_tracking():
+            self._axis_mpl, ax_histx, ax_histy, hist_data = (
+                self._get_ax_module().stx_scatter_hist(
+                    self._axis_mpl,
+                    x,
+                    y,
+                    hist_bins=hist_bins,
+                    scatter_alpha=scatter_alpha,
+                    scatter_size=scatter_size,
+                    scatter_color=scatter_color,
+                    hist_color_x=hist_color_x,
+                    hist_color_y=hist_color_y,
+                    hist_alpha=hist_alpha,
+                    scatter_ratio=scatter_ratio,
+                    **kwargs,
+                )
+            )
+
+        tracked_dict = {
+            "x": x,
+            "y": y,
+            "hist_x": hist_data["hist_x"],
+            "hist_y": hist_data["hist_y"],
+            "bin_edges_x": hist_data["bin_edges_x"],
+            "bin_edges_y": hist_data["bin_edges_y"],
+        }
+        self._track(track, id, method_name, tracked_dict, None)
+        self._apply_scitex_postprocess(method_name)
+
+        return self._axis_mpl, ax_histx, ax_histy, hist_data
+
+    def stx_heatmap(
+        self,
+        data: ArrayLike,
+        *,
+        x_labels: Optional[List[str]] = None,
+        y_labels: Optional[List[str]] = None,
+        cmap: str = "viridis",
+        cbar_label: str = "ColorBar Label",
+        value_format: str = "{x:.1f}",
+        show_annot: bool = True,
+        annot_color_lighter: str = "white",
+        annot_color_darker: str = "black",
+        track: bool = True,
+        id: Optional[str] = None,
+        **kwargs,
+    ) -> Tuple["Axes", matplotlib.image.AxesImage, matplotlib.colorbar.Colorbar]:
+        """Plot an annotated heatmap.
+
+        Parameters
+        ----------
+        data : array-like
+            2D array of values to display.
+        x_labels : list of str, optional
+            Labels for x-axis (columns).
+        y_labels : list of str, optional
+            Labels for y-axis (rows).
+        cmap : str, default 'viridis'
+            Colormap name.
+        cbar_label : str, default 'ColorBar Label'
+            Label for the colorbar.
+        value_format : str, default '{x:.1f}'
+            Format string for cell annotations.
+        show_annot : bool, default True
+            Whether to show value annotations in cells.
+        annot_color_lighter : str, default 'white'
+            Annotation color for dark backgrounds.
+        annot_color_darker : str, default 'black'
+            Annotation color for light backgrounds.
+        track : bool, default True
+            Enable data tracking for reproducibility.
+        id : str, optional
+            Unique identifier for this plot element.
+        **kwargs
+            Additional arguments passed to the heatmap function.
+
+        Returns
+        -------
+        tuple
+            (Axes, AxesImage, Colorbar) - The axes, image, and colorbar objects.
+
+        See Also
+        --------
+        sns_heatmap : DataFrame-based heatmap.
+        stx_conf_mat : Confusion matrix heatmap.
+        stx_image : Simple image display.
+
+        Examples
+        --------
+        >>> ax, im, cbar = ax.stx_heatmap(matrix, x_labels=['A', 'B'], cmap='coolwarm')
+        """
+        method_name = "stx_heatmap"
+
+        with self._no_tracking():
+            ax, im, cbar = self._get_ax_module().stx_heatmap(
+                self._axis_mpl,
+                data,
+                x_labels=x_labels,
+                y_labels=y_labels,
+                cmap=cmap,
+                cbar_label=cbar_label,
+                value_format=value_format,
+                show_annot=show_annot,
+                annot_color_lighter=annot_color_lighter,
+                annot_color_darker=annot_color_darker,
+                **kwargs,
+            )
+
+        tracked_dict = {
+            "data": data,
+            "x_labels": x_labels,
+            "y_labels": y_labels,
+        }
+        self._track(track, id, method_name, tracked_dict, None)
+        self._apply_scitex_postprocess(method_name)
+
+        return ax, im, cbar
+
+
+# EOF