scitex 2.1.3__py3-none-any.whl → 2.4.0__py3-none-any.whl

scitex/plt/styles/_plot_postprocess.py

@@ -0,0 +1,518 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-12-01 10:00:00 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/plt/styles/_plot_postprocess.py
+
+"""Post-processing styling for plot methods.
+
+This module centralizes all styling applied AFTER matplotlib methods
+are called. Each function modifies the plot result or axes in-place.
+
+All default values are loaded from SCITEX_STYLE.yaml via presets.py.
+"""
+
+import numpy as np
+from matplotlib.ticker import MaxNLocator, FixedLocator
+from matplotlib.category import StrCategoryConverter, UnitData
+
+from scitex.plt.utils import mm_to_pt
+from scitex.plt.styles.presets import SCITEX_STYLE
+
+
+# ============================================================================
+# Constants (loaded from centralized SCITEX_STYLE.yaml)
+# ============================================================================
+DEFAULT_LINE_WIDTH_MM = SCITEX_STYLE.get("trace_thickness_mm", 0.2)
+DEFAULT_MARKER_SIZE_MM = SCITEX_STYLE.get("marker_size_mm", 0.8)
+DEFAULT_N_TICKS = SCITEX_STYLE.get("n_ticks", 4) - 1  # nbins = n_ticks - 1
+SPINE_ZORDER = 1000
+CAP_WIDTH_RATIO = 1 / 3  # 33% of bar/box width
+
+
+# ============================================================================
+# Main post-processing function
+# ============================================================================
+def apply_plot_postprocess(method_name, result, ax, kwargs, args=None):
+    """Apply post-processing styling after matplotlib method call.
+
+    Args:
+        method_name: Name of the matplotlib method that was called
+        result: Return value from the matplotlib method
+        ax: The matplotlib axes
+        kwargs: Original kwargs passed to the method
+        args: Original positional args passed to the method (needed for violinplot)
+
+    Returns:
+        The result (possibly modified)
+    """
+    # Always ensure spines are on top
+    _ensure_spines_on_top(ax)
+
+    # Apply tick locator for numerical axes
+    _apply_tick_locator(ax)
+
+    # Method-specific post-processing
+    if method_name == 'pie' and result is not None:
+        _postprocess_pie(result)
+    elif method_name == 'stem' and result is not None:
+        _postprocess_stem(result)
+    elif method_name == 'violinplot' and result is not None:
+        _postprocess_violin(result, ax, kwargs, args)
+    elif method_name == 'boxplot' and result is not None:
+        _postprocess_boxplot(result, ax)
+    elif method_name == 'scatter' and result is not None:
+        _postprocess_scatter(result, kwargs)
+    elif method_name == 'bar' and result is not None:
+        _postprocess_bar(result, ax, kwargs)
+    elif method_name == 'barh' and result is not None:
+        _postprocess_barh(result, ax, kwargs)
+    elif method_name == 'errorbar' and result is not None:
+        _postprocess_errorbar(result)
+    elif method_name == 'hist' and result is not None:
+        _postprocess_hist(result, ax)
+    elif method_name == 'fill_between' and result is not None:
+        _postprocess_fill_between(result, kwargs)
+
+    return result
+
+
+# ============================================================================
+# General post-processing
+# ============================================================================
+def _ensure_spines_on_top(ax):
+    """Ensure axes spines are always drawn in front of plot elements."""
+    try:
+        ax.set_axisbelow(False)
+
+        # Set very high z-order for spines
+        for spine in ax.spines.values():
+            spine.set_zorder(SPINE_ZORDER)
+
+        # Set z-order for tick marks
+        ax.tick_params(zorder=SPINE_ZORDER)
+
+        # Ensure plot patches have lower z-order than spines
+        # But preserve intentionally set z-orders (e.g., boxplot in violin)
+        for patch in ax.patches:
+            current_z = patch.get_zorder()
+            # Only lower z-order if it's >= SPINE_ZORDER or is at matplotlib default (1)
+            if current_z >= SPINE_ZORDER:
+                patch.set_zorder(current_z - SPINE_ZORDER)
+            elif current_z == 1:
+                # Default matplotlib z-order, lower it
+                patch.set_zorder(0.5)
+            # Otherwise, preserve the intentionally set z-order
+
+        # Set axes patch behind everything
+        ax.patch.set_zorder(-1)
+    except Exception:
+        pass
+
+
+def _apply_tick_locator(ax):
+    """Apply MaxNLocator only to numerical (non-categorical) axes.
+
+    Target: 3-4 ticks per axis for clean publication figures.
+    MaxNLocator's nbins=3 gives approximately 3-4 tick marks.
+    min_n_ticks=3 ensures at least 3 ticks (never 2).
+    """
+    try:
+        def is_categorical_axis(axis):
+            if isinstance(axis.converter, StrCategoryConverter):
+                return True
+            if hasattr(axis, 'units') and isinstance(axis.units, UnitData):
+                return True
+            if isinstance(axis.get_major_locator(), FixedLocator):
+                return True
+            return False
+
+        if not is_categorical_axis(ax.xaxis):
+            ax.xaxis.set_major_locator(
+                MaxNLocator(nbins=DEFAULT_N_TICKS, min_n_ticks=3, integer=False, prune=None)
+            )
+
+        if not is_categorical_axis(ax.yaxis):
+            ax.yaxis.set_major_locator(
+                MaxNLocator(nbins=DEFAULT_N_TICKS, min_n_ticks=3, integer=False, prune=None)
+            )
+    except Exception:
+        pass
+
+
+# ============================================================================
+# Method-specific post-processing
+# ============================================================================
+def _postprocess_pie(result):
+    """Apply styling for pie charts."""
+    # pie returns (wedges, texts, autotexts) when autopct is used
+    if len(result) >= 3:
+        autotexts = result[2]
+        for autotext in autotexts:
+            autotext.set_fontsize(6)  # 6pt for inline percentages
+
+
+def _postprocess_stem(result):
+    """Apply styling for stem plots."""
+    baseline = result.baseline
+    if baseline is not None:
+        baseline.set_color('black')
+        baseline.set_linestyle('--')
+
+
+def _postprocess_errorbar(result):
+    """Apply styling for errorbar plots.
+
+    Simplifies the legend to show only a line (no caps/bars).
+    """
+    import matplotlib.legend as mlegend
+    from matplotlib.container import ErrorbarContainer
+    from matplotlib.legend_handler import HandlerErrorbar, HandlerLine2D
+
+    # Custom handler that shows only a simple line for errorbar
+    class SimpleLineHandler(HandlerErrorbar):
+        def create_artists(self, legend, orig_handle, xdescent, ydescent,
+                          width, height, fontsize, trans):
+            # Use HandlerLine2D to create just a line
+            line_handler = HandlerLine2D()
+            # Get the data line from the ErrorbarContainer
+            data_line = orig_handle[0]
+            if data_line is not None:
+                return line_handler.create_artists(
+                    legend, data_line, xdescent, ydescent,
+                    width, height, fontsize, trans
+                )
+            return []
+
+    # Register the handler globally for ErrorbarContainer
+    mlegend.Legend.update_default_handler_map({ErrorbarContainer: SimpleLineHandler()})
+
+
+def _postprocess_violin(result, ax, kwargs, args):
+    """Apply styling for violin plots with optional boxplot overlay."""
+    # Get scitex palette for coloring
+    from scitex.plt.color._PARAMS import HEX
+    palette = [HEX['blue'], HEX['red'], HEX['green'], HEX['yellow'],
+               HEX['purple'], HEX['orange'], HEX['lightblue'], HEX['pink']]
+
+    if 'bodies' in result:
+        for i, body in enumerate(result['bodies']):
+            body.set_facecolor(palette[i % len(palette)])
+            body.set_edgecolor('black')
+            body.set_linewidth(mm_to_pt(DEFAULT_LINE_WIDTH_MM))
+            body.set_alpha(1.0)
+
+    # Add boxplot overlay by default (disable with boxplot=False)
+    add_boxplot = kwargs.pop('boxplot', True)
+    if add_boxplot and args:
+        try:
+            # Get data from first positional argument
+            data = args[0]
+            # Get positions if specified, otherwise use default
+            positions = kwargs.get('positions', None)
+            if positions is None:
+                positions = range(1, len(data) + 1)
+
+            # Calculate boxplot width dynamically from violin width
+            # Get violin width from kwargs or use matplotlib default (0.5)
+            violin_widths = kwargs.get('widths', 0.5)
+            if hasattr(violin_widths, '__iter__'):
+                violin_widths = violin_widths[0] if len(violin_widths) > 0 else 0.5
+            # Boxplot width = 20% of violin width
+            boxplot_widths = violin_widths * 0.2
+
+            # Draw boxplot overlay with styling
+            line_width = mm_to_pt(DEFAULT_LINE_WIDTH_MM)
+            marker_size = mm_to_pt(DEFAULT_MARKER_SIZE_MM)
+
+            # Call matplotlib's boxplot directly to avoid recursive post-processing
+            # which would override our gray styling with the default blue
+            if hasattr(ax, '_axes_mpl'):
+                mpl_ax = ax._axes_mpl
+            else:
+                mpl_ax = ax
+            bp = mpl_ax.boxplot(
+                data,
+                positions=list(positions),
+                widths=boxplot_widths,
+                patch_artist=True,
+                manage_ticks=False,  # Don't modify existing ticks
+            )
+
+            # Style the boxplot: scitex gray fill with black edges for visibility
+            # Set high z-order so boxplot appears on top of violin bodies
+            from scitex.plt.color._PARAMS import HEX
+            boxplot_zorder = 10
+            for box in bp.get('boxes', []):
+                box.set_facecolor(HEX['gray'])  # Scitex gray fill
+                box.set_edgecolor('black')
+                box.set_alpha(1.0)
+                box.set_linewidth(line_width)
+                box.set_zorder(boxplot_zorder)
+            for median in bp.get('medians', []):
+                median.set_color('black')  # Black median line
+                median.set_linewidth(line_width)  # 0.2mm thickness
+                median.set_zorder(boxplot_zorder + 1)
+            for whisker in bp.get('whiskers', []):
+                whisker.set_color('black')
+                whisker.set_linewidth(line_width)
+                whisker.set_zorder(boxplot_zorder)
+            for cap in bp.get('caps', []):
+                cap.set_color('black')
+                cap.set_linewidth(line_width)
+                cap.set_zorder(boxplot_zorder)
+            for flier in bp.get('fliers', []):
+                flier.set_markerfacecolor('none')  # No fill (open circles)
+                flier.set_markeredgecolor('black')
+                flier.set_markersize(marker_size)  # 0.8mm
+                flier.set_markeredgewidth(line_width)  # 0.2mm
+                flier.set_zorder(boxplot_zorder + 2)
+        except Exception:
+            pass  # Silently continue if boxplot overlay fails
+
+
+def _postprocess_boxplot(result, ax):
+    """Apply styling for boxplots (standalone, not violin overlay)."""
+    # Use the centralized style_boxplot function for consistent styling
+    from scitex.plt.ax import style_boxplot
+    style_boxplot(result)
+
+    # Cap width: 33% of box width
+    if 'caps' in result and 'boxes' in result and len(result['boxes']) > 0:
+        try:
+            cap_width_pts = _calculate_cap_width_from_box(result['boxes'][0], ax)
+            for cap in result['caps']:
+                cap.set_markersize(cap_width_pts)
+        except Exception:
+            pass
+
+
+def _postprocess_scatter(result, kwargs):
+    """Apply styling for scatter plots."""
+    # Apply default 0.8mm marker size if 's' not specified
+    if 's' not in kwargs:
+        size_pt = mm_to_pt(DEFAULT_MARKER_SIZE_MM)
+        marker_area = size_pt ** 2
+        result.set_sizes([marker_area])
+
+
+def _postprocess_hist(result, ax):
+    """Apply styling for histogram plots.
+
+    Ensures histogram bars have proper edge color and alpha for visibility.
+    """
+    line_width = mm_to_pt(DEFAULT_LINE_WIDTH_MM)
+
+    # result is (n, bins, patches) tuple
+    if len(result) >= 3:
+        patches = result[2]
+        # Handle both single histogram and stacked histograms
+        if hasattr(patches, '__iter__'):
+            for patch_group in patches:
+                if hasattr(patch_group, '__iter__'):
+                    for patch in patch_group:
+                        patch.set_edgecolor('black')
+                        patch.set_linewidth(line_width)
+                        # Ensure alpha is at least 0.7 for visibility
+                        if patch.get_alpha() is None or patch.get_alpha() < 0.7:
+                            patch.set_alpha(1.0)
+                else:
+                    # Single patch
+                    patch_group.set_edgecolor('black')
+                    patch_group.set_linewidth(line_width)
+                    if patch_group.get_alpha() is None or patch_group.get_alpha() < 0.7:
+                        patch_group.set_alpha(1.0)
+
+
+def _postprocess_fill_between(result, kwargs):
+    """Apply styling for fill_between plots.
+
+    Ensures shaded regions have proper alpha for visibility.
+    """
+    # result is a PolyCollection
+    if result is not None:
+        # Set edge color to match face color or black
+        line_width = mm_to_pt(DEFAULT_LINE_WIDTH_MM)
+
+        # Only set edge if not already specified
+        if 'edgecolor' not in kwargs and 'ec' not in kwargs:
+            result.set_edgecolor('none')
+
+        # Ensure alpha is reasonable (default 0.3 is common for fill_between)
+        if 'alpha' not in kwargs:
+            result.set_alpha(0.3)
+
+
+def _postprocess_bar(result, ax, kwargs):
+    """Apply styling for bar plots with colors and error bars."""
+    # Get scitex palette for coloring (only if color not explicitly set)
+    if 'color' not in kwargs and 'c' not in kwargs:
+        from scitex.plt.color._PARAMS import HEX
+        palette = [HEX['blue'], HEX['red'], HEX['green'], HEX['yellow'],
+                   HEX['purple'], HEX['orange'], HEX['lightblue'], HEX['pink']]
+
+        line_width = mm_to_pt(DEFAULT_LINE_WIDTH_MM)
+        for i, patch in enumerate(result.patches):
+            patch.set_facecolor(palette[i % len(palette)])
+            patch.set_edgecolor('black')
+            patch.set_linewidth(line_width)
+
+    if 'yerr' not in kwargs or kwargs['yerr'] is None:
+        return
+
+    try:
+        errorbar = result.errorbar
+        if errorbar is None:
+            return
+
+        lines = errorbar.lines
+        if not lines or len(lines) < 3:
+            return
+
+        caplines = lines[1]
+        if caplines and len(caplines) >= 2:
+            # Hide lower caps (one-sided error bars)
+            caplines[0].set_visible(False)
+
+            # Adjust cap width to 33% of bar width
+            if len(result.patches) > 0:
+                cap_width_pts = _calculate_cap_width_from_bar(
+                    result.patches[0], ax, 'width'
+                )
+                for cap in caplines[1:]:
+                    cap.set_markersize(cap_width_pts)
+
+        # Make error bar lines one-sided
+        barlinecols = lines[2]
+        _make_errorbar_one_sided(barlinecols, 'vertical')
+    except Exception:
+        pass
+
+
+def _postprocess_barh(result, ax, kwargs):
+    """Apply styling for horizontal bar plots with colors and error bars."""
+    # Get scitex palette for coloring (only if color not explicitly set)
+    if 'color' not in kwargs and 'c' not in kwargs:
+        from scitex.plt.color._PARAMS import HEX
+        palette = [HEX['blue'], HEX['red'], HEX['green'], HEX['yellow'],
+                   HEX['purple'], HEX['orange'], HEX['lightblue'], HEX['pink']]
+
+        line_width = mm_to_pt(DEFAULT_LINE_WIDTH_MM)
+        for i, patch in enumerate(result.patches):
+            patch.set_facecolor(palette[i % len(palette)])
+            patch.set_edgecolor('black')
+            patch.set_linewidth(line_width)
+
+    if 'xerr' not in kwargs or kwargs['xerr'] is None:
+        return
+
+    try:
+        errorbar = result.errorbar
+        if errorbar is None:
+            return
+
+        lines = errorbar.lines
+        if not lines or len(lines) < 3:
+            return
+
+        caplines = lines[1]
+        if caplines and len(caplines) >= 2:
+            # Hide left caps (one-sided error bars)
+            caplines[0].set_visible(False)
+
+            # Adjust cap width to 33% of bar height
+            if len(result.patches) > 0:
+                cap_width_pts = _calculate_cap_width_from_bar(
+                    result.patches[0], ax, 'height'
+                )
+                for cap in caplines[1:]:
+                    cap.set_markersize(cap_width_pts)
+
+        # Make error bar lines one-sided
+        barlinecols = lines[2]
+        _make_errorbar_one_sided(barlinecols, 'horizontal')
+    except Exception:
+        pass
+
+
+# ============================================================================
+# Helper functions
+# ============================================================================
+def _calculate_cap_width_from_box(box, ax):
+    """Calculate cap width as 33% of box width in points."""
+    # Get box width from path
+    if hasattr(box, 'get_path'):
+        path = box.get_path()
+        vertices = path.vertices
+        x_coords = vertices[:, 0]
+        box_width_data = x_coords.max() - x_coords.min()
+    elif hasattr(box, 'get_xdata'):
+        x_data = box.get_xdata()
+        box_width_data = max(x_data) - min(x_data)
+    else:
+        box_width_data = 0.5  # Default
+
+    return _data_width_to_points(box_width_data, ax, 'x') * CAP_WIDTH_RATIO
+
+
+def _calculate_cap_width_from_bar(patch, ax, dimension):
+    """Calculate cap width as 33% of bar width/height in points."""
+    if dimension == 'width':
+        bar_size = patch.get_width()
+        return _data_width_to_points(bar_size, ax, 'x') * CAP_WIDTH_RATIO
+    else:  # height
+        bar_size = patch.get_height()
+        return _data_width_to_points(bar_size, ax, 'y') * CAP_WIDTH_RATIO
+
+
+def _data_width_to_points(data_size, ax, axis='x'):
+    """Convert a data-space size to points."""
+    fig = ax.get_figure()
+    bbox = ax.get_position()
+
+    if axis == 'x':
+        ax_size_inches = bbox.width * fig.get_figwidth()
+        lim = ax.get_xlim()
+    else:
+        ax_size_inches = bbox.height * fig.get_figheight()
+        lim = ax.get_ylim()
+
+    data_range = lim[1] - lim[0]
+    size_inches = (data_size / data_range) * ax_size_inches
+    return size_inches * 72  # 72 points per inch
+
+
+def _make_errorbar_one_sided(barlinecols, direction):
+    """Make error bar line segments one-sided (outward only)."""
+    if not barlinecols or len(barlinecols) == 0:
+        return
+
+    for lc in barlinecols:
+        if not hasattr(lc, 'get_segments'):
+            continue
+
+        segs = lc.get_segments()
+        new_segs = []
+        for seg in segs:
+            if len(seg) < 2:
+                continue
+
+            if direction == 'vertical':
+                # Keep upper half
+                bottom_y = min(seg[0][1], seg[1][1])
+                top_y = max(seg[0][1], seg[1][1])
+                mid_y = (bottom_y + top_y) / 2
+                new_seg = np.array([[seg[0][0], mid_y], [seg[0][0], top_y]])
+            else:  # horizontal
+                # Keep right half
+                left_x = min(seg[0][0], seg[1][0])
+                right_x = max(seg[0][0], seg[1][0])
+                mid_x = (left_x + right_x) / 2
+                new_seg = np.array([[mid_x, seg[0][1]], [right_x, seg[0][1]]])
+
+            new_segs.append(new_seg)
+
+        if new_segs:
+            lc.set_segments(new_segs)
+
+
+# EOF