scitex 2.5.0__py3-none-any.whl → 2.7.3__py3-none-any.whl

scitex/plt/_subplots/TODO.md

@@ -1,53 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-18 00:45:48
-!-- Author: ywatanabe
-!-- File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/plt/_subplots/TODO.md
-!-- --- -->
-
-1. Matplotlib plotting functions:
-   - bar
-   - barh
-   - boxplot
-   - contour
-   - errorbar
-   - eventplot
-   - fill
-   - fill_between
-   - hist
-   - imshow
-   - plot
-   - scatter
-   - violin
-   - violinplot
-
-2. Custom plotting functions:
-   - plot_box
-   - plot_conf_mat
-   - plot_ecdf
-   - plot_fillv
-   - plot_heatmap
-   - plot_image
-   - plot_joyplot
-   - plot_kde
-   - plot_line
-   - plot_mean_ci
-   - plot_mean_std
-   - plot_median_iqr
-   - plot_raster
-   - plot_rectangle
-   - plot_scatter_hist
-   - plot_shaded_line
-   - plot_violin
-   - sns_barplot
-   - sns_boxplot
-   - sns_heatmap
-   - sns_histplot
-   - sns_jointplot
-   - sns_kdeplot
-   - sns_pairplot
-   - sns_scatterplot
-   - sns_stripplot
-   - sns_swarmplot
-   - sns_violinplot
-
-<!-- EOF -->

scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py

@@ -1,537 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-06-07 15:49:20 (ywatanabe)"
-# File: /ssh:ywatanabe@sp:/home/ywatanabe/proj/.claude-worktree/scitex_repo/src/scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py
-# ----------------------------------------
-import os
-__FILE__ = __file__
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-from typing import List, Optional, Union
-
-from ....plt import ax as ax_module
-
-
-class AdjustmentMixin:
-    """Mixin class for matplotlib axis adjustments."""
-
-    def rotate_labels(
-        self,
-        x: float = None,
-        y: float = None,
-        x_ha: str = None,
-        y_ha: str = None,
-        x_va: str = None,
-        y_va: str = None,
-        auto_adjust: bool = True,
-        scientific_convention: bool = True,
-        tight_layout: bool = False,
-    ) -> None:
-        """Rotate x and y axis labels with automatic positioning.
-        
-        Parameters
-        ----------
-        x : float or None, optional
-            Rotation angle for x-axis labels in degrees. 
-            If None or 0, x-axis labels are not rotated. Default is None.
-        y : float or None, optional
-            Rotation angle for y-axis labels in degrees.
-            If None or 0, y-axis labels are not rotated. Default is None.
-        x_ha : str or None, optional
-            Horizontal alignment for x-axis labels. If None, automatically determined.
-        y_ha : str or None, optional
-            Horizontal alignment for y-axis labels. If None, automatically determined.
-        x_va : str or None, optional
-            Vertical alignment for x-axis labels. If None, automatically determined.
-        y_va : str or None, optional
-            Vertical alignment for y-axis labels. If None, automatically determined.
-        auto_adjust : bool, optional
-            Whether to automatically adjust alignment. Default is True.
-        scientific_convention : bool, optional
-            Whether to follow scientific conventions. Default is True.
-        tight_layout : bool, optional
-            Whether to apply tight_layout to prevent overlapping. Default is False.
-        """
-        self._axis_mpl = ax_module.rotate_labels(
-            self._axis_mpl, x=x, y=y, x_ha=x_ha, y_ha=y_ha,
-            x_va=x_va, y_va=y_va, auto_adjust=auto_adjust,
-            scientific_convention=scientific_convention,
-            tight_layout=tight_layout
-        )
-
-    def legend(self, *args, loc: str = "best", check_overlap: bool = False, **kwargs) -> None:
-        """Places legend at specified location, with support for outside positions.
-
-        Parameters
-        ----------
-        *args : tuple
-            Positional arguments (handles, labels) as in matplotlib
-        loc : str
-            Legend position. Default is "best" (matplotlib auto-placement).
-            Standard matplotlib positions plus:
-            - "best": Matplotlib automatic placement (default)
-            - "outer": Automatically place legend outside plot area (right side)
-            - "separate": Save legend as a separate figure file
-            - upper/lower/center variants: e.g. "upper right out", "lower left out"
-            - directional shortcuts: "right", "left", "upper", "lower"
-            - center variants: "center right out", "center left out"
-            - alternative formats: "right upper out", "left lower out" etc.
-        check_overlap : bool
-            If True, checks for overlap between legend and data after placement.
-            Issues warning with suggestion if significant overlap detected.
-        **kwargs : dict
-            Additional keyword arguments passed to legend()
-            For "separate": can include 'filename' (default: 'legend.png')
-        """
-        import matplotlib.pyplot as plt
-
-        # Handle special cases
-        if loc == "outer":
-            # Place legend outside on the right, adjusting figure to make room
-            legend = self._axis_mpl.legend(
-                *args,
-                loc='center left',
-                bbox_to_anchor=(1.02, 0.5),
-                **kwargs
-            )
-            # Adjust figure to prevent legend cutoff
-            if hasattr(self, '_figure_wrapper') and self._figure_wrapper:
-                self._figure_wrapper._fig_mpl.tight_layout()
-                self._figure_wrapper._fig_mpl.subplots_adjust(right=0.85)
-            return legend
-            
-        elif loc == "separate":
-            # Set flag to save legend separately when figure is saved
-            import warnings
-            
-            handles, labels = self._axis_mpl.get_legend_handles_labels()
-            if not handles:
-                warnings.warn("No legend handles found. Create plots with labels first.")
-                return None
-            
-            # Store legend params for later use during save
-            fig = self._axis_mpl.get_figure()
-            if not hasattr(fig, '_separate_legend_params'):
-                fig._separate_legend_params = []
-            
-            # Extract separate-specific kwargs
-            figsize = kwargs.pop('figsize', (4, 3))
-            dpi = kwargs.pop('dpi', 150)
-            frameon = kwargs.pop('frameon', True)
-            fancybox = kwargs.pop('fancybox', True)
-            shadow = kwargs.pop('shadow', True)
-            
-            # Store parameters for this axes
-            # Include axis index or name for unique filenames
-            axis_id = None
-            
-            # Try to find axis index in parent figure
-            try:
-                fig_axes = fig.get_axes()
-                for idx, ax in enumerate(fig_axes):
-                    if ax is self._axis_mpl:
-                        axis_id = f"ax_{idx:02d}"
-                        break
-            except:
-                pass
-            
-            # If not found, try subplot spec
-            if axis_id is None and hasattr(self._axis_mpl, 'get_subplotspec'):
-                try:
-                    spec = self._axis_mpl.get_subplotspec()
-                    if spec is not None:
-                        # Get grid shape and position
-                        gridspec = spec.get_gridspec()
-                        nrows, ncols = gridspec.get_geometry()
-                        rowspan = spec.rowspan
-                        colspan = spec.colspan
-                        # Calculate flat index from row/col position
-                        row_start = rowspan.start if hasattr(rowspan, 'start') else rowspan
-                        col_start = colspan.start if hasattr(colspan, 'start') else colspan
-                        flat_idx = row_start * ncols + col_start
-                        axis_id = f"ax_{flat_idx:02d}"
-                except:
-                    pass
-            
-            # Fallback to sequential numbering
-            if axis_id is None:
-                axis_id = f"ax_{len(fig._separate_legend_params):02d}"
-                
-            fig._separate_legend_params.append({
-                'axis': self._axis_mpl,
-                'axis_id': axis_id,
-                'handles': handles,
-                'labels': labels,
-                'figsize': figsize,
-                'dpi': dpi,
-                'frameon': frameon,
-                'fancybox': fancybox,
-                'shadow': shadow,
-                'kwargs': kwargs
-            })
-            
-            # Remove legend from main figure immediately
-            if self._axis_mpl.get_legend():
-                self._axis_mpl.get_legend().remove()
-            
-            return None
-
-        # Original outside positions
-        outside_positions = {
-            # Upper right variants
-            "upper right out": ("center left", (1.15, 0.85)),
-            "right upper out": ("center left", (1.15, 0.85)),
-            # Center right variants
-            "center right out": ("center left", (1.15, 0.5)),
-            "right out": ("center left", (1.15, 0.5)),
-            "right": ("center left", (1.05, 0.5)),
-            # Lower right variants
-            "lower right out": ("center left", (1.15, 0.15)),
-            "right lower out": ("center left", (1.15, 0.15)),
-            # Upper left variants
-            "upper left out": ("center right", (-0.25, 0.85)),
-            "left upper out": ("center right", (-0.25, 0.85)),
-            # Center left variants
-            "center left out": ("center right", (-0.25, 0.5)),
-            "left out": ("center right", (-0.25, 0.5)),
-            "left": ("center right", (-0.15, 0.5)),
-            # Lower left variants
-            "lower left out": ("center right", (-0.25, 0.15)),
-            "left lower out": ("center right", (-0.25, 0.15)),
-            # Upper center variants
-            "upper center out": ("lower center", (0.5, 1.25)),
-            "upper out": ("lower center", (0.5, 1.25)),
-            # Lower center variants
-            "lower center out": ("upper center", (0.5, -0.25)),
-            "lower out": ("upper center", (0.5, -0.25)),
-        }
-
-        # Place the legend
-        if loc in outside_positions:
-            location, bbox = outside_positions[loc]
-            legend_obj = self._axis_mpl.legend(*args, loc=location, bbox_to_anchor=bbox, **kwargs)
-        else:
-            legend_obj = self._axis_mpl.legend(*args, loc=loc, **kwargs)
-
-        # Check for overlap if requested
-        if check_overlap and legend_obj is not None:
-            self._check_legend_overlap(legend_obj)
-
-        return legend_obj
-
-    def _check_legend_overlap(self, legend_obj):
-        """Check if legend overlaps with plotted data and issue warning if needed.
-
-        Parameters
-        ----------
-        legend_obj : matplotlib.legend.Legend
-            The legend object to check for overlap
-        """
-        import warnings
-        import matplotlib.transforms as transforms
-
-        try:
-            # Get the legend's bounding box in display coordinates
-            fig = self._axis_mpl.get_figure()
-            fig.canvas.draw()  # Force draw to get accurate bounding boxes
-
-            legend_bbox = legend_obj.get_window_extent(fig.canvas.get_renderer())
-
-            # Convert to axis coordinates for easier comparison
-            inv_transform = self._axis_mpl.transData.inverted()
-            legend_bbox_data = legend_bbox.transformed(inv_transform)
-
-            # Get data bounding boxes for all artists (lines, scatter, etc.)
-            data_bboxes = []
-
-            for line in self._axis_mpl.get_lines():
-                if line.get_visible():
-                    try:
-                        data = line.get_xydata()
-                        if len(data) > 0:
-                            data_bboxes.append(data)
-                    except:
-                        pass
-
-            for collection in self._axis_mpl.collections:
-                if collection.get_visible():
-                    try:
-                        offsets = collection.get_offsets()
-                        if len(offsets) > 0:
-                            data_bboxes.append(offsets)
-                    except:
-                        pass
-
-            # Check for overlap
-            if data_bboxes:
-                import numpy as np
-                all_data = np.vstack(data_bboxes)
-
-                # Count how many data points fall within legend bbox
-                x_overlap = (all_data[:, 0] >= legend_bbox_data.x0) & (all_data[:, 0] <= legend_bbox_data.x1)
-                y_overlap = (all_data[:, 1] >= legend_bbox_data.y0) & (all_data[:, 1] <= legend_bbox_data.y1)
-                overlap_points = np.sum(x_overlap & y_overlap)
-
-                # Calculate overlap percentage
-                overlap_pct = (overlap_points / len(all_data)) * 100
-
-                # Warn if significant overlap (>5% of data points)
-                if overlap_pct > 5:
-                    warnings.warn(
-                        f"Legend overlaps with {overlap_pct:.1f}% of data points. "
-                        f"Consider using:\n"
-                        f"  - ax.legend(loc='outer')  # Place outside plot area\n"
-                        f"  - ax.legend(loc='separate')  # Save as separate file\n"
-                        f"  - Manually adjust with loc='upper left', 'lower right', etc.",
-                        UserWarning,
-                        stacklevel=3
-                    )
-                    return True  # Overlap detected
-
-        except Exception as e:
-            # Silently fail if overlap detection doesn't work
-            # (Some plot types may not support this)
-            pass
-
-        return False  # No significant overlap
-
-    def set_xyt(
-        self,
-        x: Optional[str] = None,
-        y: Optional[str] = None,
-        t: Optional[str] = None,
-        format_labels: bool = True,
-    ) -> None:
-        self._axis_mpl = ax_module.set_xyt(
-            self._axis_mpl,
-            x=x,
-            y=y,
-            t=t,
-            format_labels=format_labels,
-        )
-
-    def set_xytc(
-        self,
-        x: Optional[str] = None,
-        y: Optional[str] = None,
-        t: Optional[str] = None,
-        c: Optional[str] = None,
-        format_labels: bool = True,
-    ) -> None:
-        """Set xlabel, ylabel, title, and caption for automatic saving.
-
-        Parameters
-        ----------
-        x : str, optional
-            X-axis label
-        y : str, optional
-            Y-axis label
-        t : str, optional
-            Title
-        c : str, optional
-            Caption to be saved automatically with scitex.io.save()
-        format_labels : bool, optional
-            Whether to apply automatic formatting, by default True
-        """
-        self._axis_mpl = ax_module.set_xytc(
-            self._axis_mpl,
-            x=x,
-            y=y,
-            t=t,
-            c=c,
-            format_labels=format_labels,
-        )
-
-        # Store caption in this wrapper for easy access
-        if c is not False and c is not None:
-            self._scitex_caption = c
-
-    def set_supxyt(
-        self,
-        xlabel: Optional[str] = None,
-        ylabel: Optional[str] = None,
-        title: Optional[str] = None,
-        format_labels: bool = True,
-    ) -> None:
-        self._axis_mpl = ax_module.set_supxyt(
-            self._axis_mpl,
-            xlabel=xlabel,
-            ylabel=ylabel,
-            title=title,
-            format_labels=format_labels,
-        )
-
-    def set_supxytc(
-        self,
-        xlabel: Optional[str] = None,
-        ylabel: Optional[str] = None,
-        title: Optional[str] = None,
-        caption: Optional[str] = None,
-        format_labels: bool = True,
-    ) -> None:
-        """Set figure-level xlabel, ylabel, title, and caption for automatic saving.
-
-        Parameters
-        ----------
-        xlabel : str, optional
-            Figure-level X-axis label
-        ylabel : str, optional
-            Figure-level Y-axis label
-        title : str, optional
-            Figure-level title (suptitle)
-        caption : str, optional
-            Figure-level caption to be saved automatically with scitex.io.save()
-        format_labels : bool, optional
-            Whether to apply automatic formatting, by default True
-        """
-        self._axis_mpl = ax_module.set_supxytc(
-            self._axis_mpl,
-            xlabel=xlabel,
-            ylabel=ylabel,
-            title=title,
-            caption=caption,
-            format_labels=format_labels,
-        )
-
-        # Store figure-level caption for easy access
-        if caption is not False and caption is not None:
-            fig = self._axis_mpl.get_figure()
-            fig._scitex_main_caption = caption
-
-    def set_meta(
-        self,
-        caption=None,
-        methods=None,
-        stats=None,
-        keywords=None,
-        experimental_details=None,
-        journal_style=None,
-        significance=None,
-        **kwargs
-    ) -> None:
-        """Set comprehensive scientific metadata with YAML export capability.
-
-        Parameters
-        ----------
-        caption : str, optional
-            Figure caption text
-        methods : str, optional
-            Experimental methods description
-        stats : str, optional
-            Statistical analysis details
-        keywords : List[str], optional
-            Keywords for categorization
-        experimental_details : Dict[str, Any], optional
-            Structured experimental parameters
-        journal_style : str, optional
-            Target journal style
-        significance : str, optional
-            Significance statement
-        **kwargs : additional metadata
-            Any additional metadata fields
-        """
-        self._axis_mpl = ax_module.set_meta(
-            self._axis_mpl,
-            caption=caption,
-            methods=methods,
-            stats=stats,
-            keywords=keywords,
-            experimental_details=experimental_details,
-            journal_style=journal_style,
-            significance=significance,
-            **kwargs
-        )
-
-    def set_figure_meta(
-        self,
-        caption=None,
-        methods=None,
-        stats=None,
-        significance=None,
-        funding=None,
-        conflicts=None,
-        data_availability=None,
-        **kwargs
-    ) -> None:
-        """Set figure-level metadata for multi-panel figures.
-
-        Parameters
-        ----------
-        caption : str, optional
-            Figure-level caption
-        methods : str, optional
-            Overall experimental methods
-        stats : str, optional
-            Overall statistical approach
-        significance : str, optional
-            Significance and implications
-        funding : str, optional
-            Funding acknowledgments
-        conflicts : str, optional
-            Conflict of interest statement
-        data_availability : str, optional
-            Data availability statement
-        **kwargs : additional metadata
-            Any additional figure-level metadata
-        """
-        self._axis_mpl = ax_module.set_figure_meta(
-            self._axis_mpl,
-            caption=caption,
-            methods=methods,
-            stats=stats,
-            significance=significance,
-            funding=funding,
-            conflicts=conflicts,
-            data_availability=data_availability,
-            **kwargs
-        )
-
-    def set_ticks(
-        self,
-        xvals: Optional[List[Union[int, float]]] = None,
-        xticks: Optional[List[str]] = None,
-        yvals: Optional[List[Union[int, float]]] = None,
-        yticks: Optional[List[str]] = None,
-    ) -> None:
-        self._axis_mpl = ax_module.set_ticks(
-            self._axis_mpl,
-            xvals=xvals,
-            xticks=xticks,
-            yvals=yvals,
-            yticks=yticks,
-        )
-
-    def set_n_ticks(self, n_xticks: int = 4, n_yticks: int = 4) -> None:
-        self._axis_mpl = ax_module.set_n_ticks(
-            self._axis_mpl, n_xticks=n_xticks, n_yticks=n_yticks
-        )
-
-    def hide_spines(
-        self,
-        top: bool = True,
-        bottom: bool = False,
-        left: bool = False,
-        right: bool = True,
-        ticks: bool = False,
-        labels: bool = False,
-    ) -> None:
-        self._axis_mpl = ax_module.hide_spines(
-            self._axis_mpl,
-            top=top,
-            bottom=bottom,
-            left=left,
-            right=right,
-            ticks=ticks,
-            labels=labels,
-        )
-
-    def extend(self, x_ratio: float = 1.0, y_ratio: float = 1.0) -> None:
-        self._axis_mpl = ax_module.extend(
-            self._axis_mpl, x_ratio=x_ratio, y_ratio=y_ratio
-        )
-
-    def shift(self, dx: float = 0, dy: float = 0) -> None:
-        self._axis_mpl = ax_module.shift(self._axis_mpl, dx=dx, dy=dy)
-
-# EOF