scitex 2.0.0__py2.py3-none-any.whl

scitex/plt/ax/__init__.py

@@ -0,0 +1,114 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-05-02 20:12:46 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/plt/ax/__init__.py
+# ----------------------------------------
+import os
+
+__FILE__ = "./src/scitex/plt/ax/__init__.py"
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+
+# Adjust
+from ._style._add_marginal_ax import add_marginal_ax
+from ._style._add_panel import add_panel, panel
+from ._style._extend import extend
+from ._style._force_aspect import force_aspect
+from ._style._format_label import format_label
+from ._style._hide_spines import hide_spines
+from ._style._show_spines import (
+    show_spines,
+    show_all_spines,
+    show_classic_spines,
+    show_box_spines,
+    toggle_spines,
+    scientific_spines,
+    clean_spines,
+)
+from ._style._map_ticks import map_ticks
+from ._style._rotate_labels import rotate_labels
+from ._style._sci_note import sci_note
+from ._style._set_n_ticks import set_n_ticks
+from ._style._set_size import set_size
+from ._style._set_supxyt import set_supxyt
+from ._style._set_ticks import set_ticks
+from ._style._set_xyt import set_xyt
+from ._style._shift import shift
+from ._style._share_axes import (
+    get_global_xlim,
+    get_global_ylim,
+    set_xlims,
+    set_ylims,
+    sharex,
+    sharexy,
+    sharey,
+)
+from ._style._set_log_scale import (
+    set_log_scale,
+    smart_log_limits,
+    add_log_scale_indicator,
+)
+
+# Plot
+from ._plot._plot_heatmap import plot_heatmap
+from ._plot._plot_circular_hist import plot_circular_hist
+from ._plot._plot_conf_mat import plot_conf_mat
+from ._plot._plot_cube import plot_cube
+from ._plot._plot_ecdf import plot_ecdf
+from ._plot._plot_fillv import plot_fillv
+from ._plot._plot_violin import plot_violin
+from ._plot._plot_image import plot_image
+from ._plot._plot_joyplot import plot_joyplot
+from ._plot._plot_raster import plot_raster
+from ._plot._plot_rectangle import plot_rectangle
+from ._plot._plot_scatter_hist import plot_scatter_hist
+from ._plot._plot_shaded_line import plot_shaded_line
+from ._plot._plot_statistical_shaded_line import (
+    plot_line,
+    plot_mean_std,
+    plot_mean_ci,
+    plot_median_iqr,
+)
+
+
+# ################################################################################
+# # For Matplotlib Compatibility
+# ################################################################################
+# import matplotlib.pyplot.axis as counter_part
+# _local_module_attributes = list(globals().keys())
+# print(_local_module_attributes)
+
+# def __getattr__(name):
+#     """
+#     Fallback to fetch attributes from matplotlib.pyplot
+#     if they are not defined directly in this module.
+#     """
+#     try:
+#         # Get the attribute from matplotlib.pyplot
+#         return getattr(counter_part, name)
+#     except AttributeError:
+#         # Raise the standard error if not found in pyplot either
+#         raise AttributeError(
+#             f"module '{__name__}' nor matplotlib.pyplot has attribute '{name}'"
+#         ) from None
+
+# def __dir__():
+#     """
+#     Provide combined directory for tab completion, including
+#     attributes from this module and matplotlib.pyplot.
+#     """
+#     # Get attributes defined explicitly in this module
+#     local_attrs = set(_local_module_attributes)
+#     # Get attributes from matplotlib.pyplot
+#     pyplot_attrs = set(dir(counter_part))
+#     # Return the sorted union
+#     return sorted(local_attrs.union(pyplot_attrs))
+
+# """
+# import matplotlib.pyplot as plt
+# import scitex.plt as mplt
+
+# print(set(dir(mplt.ax)) - set(dir(plt.axis)))
+# """
+
+# EOF

scitex/plt/ax/_plot/__init__.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-05-02 20:12:19 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/plt/ax/_plot/__init__.py
+# ----------------------------------------
+import os
+
+__FILE__ = "./src/scitex/plt/ax/_plot/__init__.py"
+__DIR__ = os.path.dirname(__FILE__)
+
+from ._plot_scatter_hist import plot_scatter_hist
+from ._plot_heatmap import plot_heatmap
+from ._plot_circular_hist import plot_circular_hist
+from ._plot_conf_mat import plot_conf_mat
+from ._plot_cube import plot_cube
+from ._plot_ecdf import plot_ecdf
+from ._plot_fillv import plot_fillv
+from ._plot_violin import plot_violin, sns_plot_violin
+from ._plot_image import plot_image
+from ._plot_joyplot import plot_joyplot
+from ._plot_raster import plot_raster
+from ._plot_rectangle import plot_rectangle
+from ._plot_shaded_line import plot_shaded_line, _plot_single_shaded_line
+from ._plot_statistical_shaded_line import (
+    plot_line,
+    plot_mean_std,
+    plot_mean_ci,
+    plot_median_iqr,
+)
+
+__all__ = [
+    "plot_scatter_hist",
+    "plot_heatmap",
+    "plot_circular_hist",
+    "plot_conf_mat",
+    "plot_cube",
+    "plot_ecdf",
+    "plot_fillv",
+    "plot_violin",
+    "sns_plot_violin",
+    "plot_image",
+    "plot_joyplot",
+    "plot_raster",
+    "plot_rectangle",
+    "plot_shaded_line",
+    "_plot_single_shaded_line",
+    "plot_line",
+    "plot_mean_std",
+    "plot_mean_ci",
+    "plot_median_iqr",
+]
+
+# EOF

scitex/plt/ax/_plot/_plot_circular_hist.py

@@ -0,0 +1,124 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-05-01 15:21:48 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/plt/ax/_plot/_plot_circular_hist.py
+# ----------------------------------------
+import os
+
+__FILE__ = "./src/scitex/plt/ax/_plot/_plot_circular_hist.py"
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+
+# Time-stamp: "2024-02-03 13:10:50 (ywatanabe)"
+import matplotlib
+import numpy as np
+from ....plt.utils import assert_valid_axis
+
+
+def plot_circular_hist(
+    axis,
+    radians,
+    bins=16,
+    density=True,
+    offset=0,
+    gaps=True,
+    color=None,
+    range_bias=0,
+):
+    """
+    Example:
+        fig, ax = plt.subplots(subplot_kw=dict(projection="polar"))
+        ax = scitex.plt.plot_circular_hist(ax, radians)
+    Produce a circular histogram of angles on ax.
+
+    Parameters
+    ----------
+    ax : matplotlib.axes._subplots.PolarAxesSubplot or scitex.plt._subplots.AxisWrapper
+        axis instance created with subplot_kw=dict(projection='polar').
+
+    radians : array
+        Angles to plot, expected in units of radians.
+
+    bins : int, optional
+        Defines the number of equal-width bins in the range. The default is 16.
+
+    density : bool, optional
+        If True plot frequency proportional to area. If False plot frequency
+        proportional to radius. The default is True.
+
+    offset : float, optional
+        Sets the offset for the location of the 0 direction in units of
+        radians. The default is 0.
+
+    gaps : bool, optional
+        Whether to allow gaps between bins. When gaps = False the bins are
+        forced to partition the entire [-pi, pi] range. The default is True.
+
+    Returns
+    -------
+    n : array or list of arrays
+        The number of values in each bin.
+
+    bins : array
+        The edges of the bins.
+
+    patches : `.BarContainer` or list of a single `.Polygon`
+        Container of individual artists used to create the histogram
+        or list of such containers if there are multiple input datasets.
+    """
+    assert_valid_axis(axis, "First argument must be a matplotlib axis or scitex axis wrapper")
+
+    # Wrap angles to [-pi, pi)
+    radians = (radians + np.pi) % (2 * np.pi) - np.pi
+
+    # Force bins to partition entire circle
+    if not gaps:
+        bins = np.linspace(-np.pi, np.pi, num=bins + 1)
+
+    # Bin data and record counts
+    n, bins = np.histogram(
+        radians, bins=bins, range=(-np.pi + range_bias, np.pi + range_bias)
+    )
+
+    # Compute width of each bin
+    widths = np.diff(bins)
+
+    # By default plot frequency proportional to area
+    if density:
+        # Area to assign each bin
+        area = n / radians.size
+        # Calculate corresponding bin radius
+        radius = (area / np.pi) ** 0.5
+    # Otherwise plot frequency proportional to radius
+    else:
+        radius = n
+
+    mean_val = np.nanmean(radians)
+    std_val = np.nanstd(radians)
+    axis.axvline(mean_val, color=color)
+    axis.text(mean_val, 1, std_val)
+
+    # Plot data on ax
+    patches = axis.bar(
+        bins[:-1],
+        radius,
+        zorder=1,
+        align="edge",
+        width=widths,
+        edgecolor=color,
+        alpha=0.9,
+        fill=False,
+        linewidth=1,
+    )
+
+    # Set the direction of the zero angle
+    axis.set_theta_offset(offset)
+
+    # Remove ylabels for area plots (they are mostly obstructive)
+    if density:
+        axis.set_yticks([])
+
+    return n, bins, patches
+
+
+# EOF

scitex/plt/ax/_plot/_plot_conf_mat.py

@@ -0,0 +1,136 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-05-18 15:08:16 (ywatanabe)"
+# File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/plt/ax/_plot/_plot_conf_mat.py
+# ----------------------------------------
+import os
+
+__FILE__ = "./src/scitex/plt/ax/_plot/_plot_conf_mat.py"
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+
+from typing import List, Optional, Tuple, Union
+
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import seaborn as sns
+
+from ...utils._calc_bacc_from_conf_mat import calc_bacc_from_conf_mat
+from ...utils import assert_valid_axis
+from .._style._extend import extend as scitex_plt_extend
+
+
+def plot_conf_mat(
+    axis: plt.Axes,
+    data: Union[np.ndarray, pd.DataFrame],
+    x_labels: Optional[List[str]] = None,
+    y_labels: Optional[List[str]] = None,
+    title: str = "Confusion Matrix",
+    cmap: str = "Blues",
+    cbar: bool = True,
+    cbar_kw: dict = {},
+    label_rotation_xy: Tuple[float, float] = (15, 15),
+    x_extend_ratio: float = 1.0,
+    y_extend_ratio: float = 1.0,
+    calc_bacc: bool = False,
+    **kwargs,
+) -> Union[plt.Axes, Tuple[plt.Axes, float]]:
+    """Creates a confusion matrix heatmap with optional balanced accuracy.
+
+    Parameters
+    ----------
+    axis : plt.Axes or scitex.plt._subplots._AxisWrapper.AxisWrapper
+        Matplotlib axes or scitex axis wrapper to plot on
+    data : Union[np.ndarray, pd.DataFrame]
+        Confusion matrix data
+    x_labels : Optional[List[str]], optional
+        Labels for predicted classes
+    y_labels : Optional[List[str]], optional
+        Labels for true classes
+    title : str, optional
+        Plot title
+    cmap : str, optional
+        Colormap name
+    cbar : bool, optional
+        Whether to show colorbar
+    cbar_kw : dict, optional
+        Colorbar parameters
+    label_rotation_xy : Tuple[float, float], optional
+        (x,y) label rotation angles
+    x_extend_ratio : float, optional
+        X-axis extension ratio
+    y_extend_ratio : float, optional
+        Y-axis extension ratio
+    calc_bacc : bool, optional
+        Calculate Balanced Accuracy from Confusion Matrix
+
+    Returns
+    -------
+    Union[plt.Axes, Tuple[plt.Axes, float]] or Union[scitex.plt._subplots._AxisWrapper.AxisWrapper, Tuple[scitex.plt._subplots._AxisWrapper.AxisWrapper, float]]
+        Axes object and optionally balanced accuracy
+
+    Example
+    -------
+    >>> data = np.array([[10, 2, 0], [1, 15, 3], [0, 2, 20]])
+    >>> fig, ax = plt.subplots()
+    >>> ax, bacc = plot_conf_mat(ax, data, x_labels=['A','B','C'],
+    ...                     y_labels=['X','Y','Z'], calc_bacc=True)
+    >>> print(f"Balanced Accuracy: {bacc:.3f}")
+    Balanced Accuracy: 0.889
+    """
+
+    assert_valid_axis(axis, "First argument must be a matplotlib axis or scitex axis wrapper")
+
+    if not isinstance(data, pd.DataFrame):
+        data = pd.DataFrame(data)
+
+    bacc_val = calc_bacc_from_conf_mat(data.values)
+    title = f"{title} (bACC = {bacc_val:.3f})"
+
+    res = sns.heatmap(
+        data,
+        ax=axis,
+        cmap=cmap,
+        annot=True,
+        fmt=",d",
+        cbar=False,
+        vmin=0,
+        **kwargs,
+    )
+
+    res.invert_yaxis()
+
+    for _, spine in res.spines.items():
+        spine.set_visible(False)
+
+    axis.set_xlabel("Predicted label")
+    axis.set_ylabel("True label")
+    axis.set_title(title)
+
+    if x_labels is not None:
+        axis.set_xticklabels(x_labels)
+    if y_labels is not None:
+        axis.set_yticklabels(y_labels)
+
+    axis = scitex_plt_extend(axis, x_extend_ratio, y_extend_ratio)
+    if data.shape[0] == data.shape[1]:
+        axis.set_box_aspect(1)
+        axis.set_xticklabels(
+            axis.get_xticklabels(),
+            rotation=label_rotation_xy[0],
+            fontdict={"verticalalignment": "top"},
+        )
+        axis.set_yticklabels(
+            axis.get_yticklabels(),
+            rotation=label_rotation_xy[1],
+            fontdict={"horizontalalignment": "right"},
+        )
+
+    if calc_bacc:
+        return axis, bacc_val
+    else:
+        return axis, None
+
+# EOF

scitex/plt/ax/_plot/_plot_cube.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-05-01 15:21:37 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/plt/ax/_plot/_plot_cube.py
+# ----------------------------------------
+import os
+
+__FILE__ = "./src/scitex/plt/ax/_plot/_plot_cube.py"
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+
+from itertools import combinations, product
+
+import numpy as np
+
+
+def plot_cube(ax, xlim, ylim, zlim, c="blue", alpha=1.0):
+    """
+    Plot a 3D cube on the given axis.
+
+    Args:
+        ax: Matplotlib 3D axis
+        xlim: Range for x-axis as a tuple (min, max)
+        ylim: Range for y-axis as a tuple (min, max)
+        zlim: Range for z-axis as a tuple (min, max)
+        c: Color of the cube edges (default: 'blue')
+        alpha: Transparency of the cube edges (default: 1.0)
+
+    Returns:
+        Matplotlib axis with the cube plotted
+    """
+    # Validate inputs
+    assert hasattr(ax, "plot3D"), "The axis must be a 3D axis with plot3D method"
+    assert len(xlim) == 2, "xlim must be a tuple of (min, max)"
+    assert len(ylim) == 2, "ylim must be a tuple of (min, max)"
+    assert len(zlim) == 2, "zlim must be a tuple of (min, max)"
+    assert xlim[0] < xlim[1], "xlim[0] must be less than xlim[1]"
+    assert ylim[0] < ylim[1], "ylim[0] must be less than ylim[1]"
+    assert zlim[0] < zlim[1], "zlim[0] must be less than zlim[1]"
+
+    # Get all corners of the cube
+    corners = np.array(list(product(xlim, ylim, zlim)))
+
+    # Draw edges between corners
+    for start, end in combinations(corners, 2):
+        # Check if the points form an edge (differ in exactly one dimension)
+        if np.sum(np.abs(start - end)) == xlim[1] - xlim[0]:
+            ax.plot3D(*zip(start, end), c=c, linewidth=3, alpha=alpha)
+        if np.sum(np.abs(start - end)) == ylim[1] - ylim[0]:
+            ax.plot3D(*zip(start, end), c=c, linewidth=3, alpha=alpha)
+        if np.sum(np.abs(start - end)) == zlim[1] - zlim[0]:
+            ax.plot3D(*zip(start, end), c=c, linewidth=3, alpha=alpha)
+
+    return ax
+
+
+# EOF

scitex/plt/ax/_plot/_plot_ecdf.py

@@ -0,0 +1,84 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-05-01 20:17:59 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/plt/ax/_plot/_plot_ecdf.py
+# ----------------------------------------
+import os
+
+__FILE__ = "./src/scitex/plt/ax/_plot/_plot_ecdf.py"
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+
+import warnings
+
+import matplotlib
+import numpy as np
+
+from ....pd._force_df import force_df as scitex_pd_force_df
+from ....plt.utils import assert_valid_axis
+
+
+def plot_ecdf(axis, data, **kwargs):
+    """Plot Empirical Cumulative Distribution Function (ECDF).
+
+    The ECDF shows the proportion of data points less than or equal to each value,
+    representing the empirical estimate of the cumulative distribution function.
+
+    Parameters
+    ----------
+    axis : matplotlib.axes.Axes or scitex.plt._subplots.AxisWrapper
+        Matplotlib axis or scitex axis wrapper to plot on
+    data : array-like
+        Data to compute and plot ECDF for. NaN values are ignored.
+    **kwargs : dict
+        Additional arguments to pass to plot function
+
+    Returns
+    -------
+    tuple
+        (axis, DataFrame) containing the plot and data
+    """
+    assert_valid_axis(axis, "First argument must be a matplotlib axis or scitex axis wrapper")
+
+    # Flatten and remove NaN values
+    data = np.hstack(data)
+
+    # Warnings
+    if np.isnan(data).any():
+        warnings.warn("NaN value are ignored for ECDF plot.")
+    data = data[~np.isnan(data)]
+    nn = len(data)
+
+    # Sort the data and compute the ECDF values
+    data_sorted = np.sort(data)
+    ecdf_perc = 100 * np.arange(1, len(data_sorted) + 1) / len(data_sorted)
+
+    # Create the pseudo x-axis for step plotting
+    x_step = np.repeat(data_sorted, 2)[1:]
+    y_step = np.repeat(ecdf_perc, 2)[:-1]
+
+    # Plot the ECDF using steps
+    axis.plot(x_step, y_step, drawstyle="steps-post", **kwargs)
+
+    # Scatter the original data points
+    axis.plot(data_sorted, ecdf_perc, marker=".", linestyle="none")
+
+    # Set ylim, xlim, and aspect ratio
+    axis.set_ylim(0, 100)
+    axis.set_xlim(0, 1.0)
+
+    # Create a DataFrame to hold the ECDF data
+    df = scitex_pd_force_df(
+        {
+            "x": data_sorted,
+            "y": ecdf_perc,
+            "n": nn,
+            "x_step": x_step,
+            "y_step": y_step,
+        }
+    )
+
+    return axis, df
+
+
+# EOF

scitex/plt/ax/_plot/_plot_fillv.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-04-30 21:26:45 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/plt/ax/_plot_fillv.py
+# ----------------------------------------
+import os
+
+__FILE__ = "./src/scitex/plt/ax/_plot_fillv.py"
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+
+import matplotlib
+import numpy as np
+from ....plt.utils import assert_valid_axis
+
+
+def plot_fillv(axes, starts, ends, color="red", alpha=0.2):
+    """
+    Fill between specified start and end intervals on an axis or array of axes.
+
+    Parameters
+    ----------
+    axes : matplotlib.axes.Axes or scitex.plt._subplots.AxisWrapper or numpy.ndarray of axes
+        The axis object(s) to fill intervals on.
+    starts : array-like
+        Array-like of start positions.
+    ends : array-like
+        Array-like of end positions.
+    color : str, optional
+        The color to use for the filled regions. Default is "red".
+    alpha : float, optional
+        The alpha blending value, between 0 (transparent) and 1 (opaque). Default is 0.2.
+
+    Returns
+    -------
+    list
+        List of axes with filled intervals.
+    """
+
+    is_axes = isinstance(axes, np.ndarray)
+
+    axes = axes if isinstance(axes, np.ndarray) else [axes]
+
+    for ax in axes:
+        assert_valid_axis(ax, "First argument must be a matplotlib axis or scitex axis wrapper")
+        for start, end in zip(starts, ends):
+            ax.axvspan(start, end, color=color, alpha=alpha)
+
+    if not is_axes:
+        return axes[0]
+    else:
+        return axes
+
+
+# EOF