@synsci/cli-darwin-x64-baseline 1.1.77 → 1.1.78

package/bin/skills/scientific-visualization/scripts/style_presets.py

@@ -0,0 +1,416 @@
+#!/usr/bin/env python3
+"""
+Matplotlib Style Presets for Publication-Ready Scientific Figures
+
+This module provides pre-configured matplotlib styles optimized for
+different journals and use cases.
+"""
+
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+from typing import Optional, Dict, Any
+
+
+# Okabe-Ito colorblind-friendly palette
+OKABE_ITO_COLORS = [
+    '#E69F00',  # Orange
+    '#56B4E9',  # Sky Blue
+    '#009E73',  # Bluish Green
+    '#F0E442',  # Yellow
+    '#0072B2',  # Blue
+    '#D55E00',  # Vermillion
+    '#CC79A7',  # Reddish Purple
+    '#000000'   # Black
+]
+
+# Paul Tol palettes
+TOL_BRIGHT = ['#4477AA', '#EE6677', '#228833', '#CCBB44', '#66CCEE', '#AA3377', '#BBBBBB']
+TOL_MUTED = ['#332288', '#88CCEE', '#44AA99', '#117733', '#999933', '#DDCC77', '#CC6677', '#882255', '#AA4499']
+TOL_HIGH_CONTRAST = ['#004488', '#DDAA33', '#BB5566']
+
+# Wong palette
+WONG_COLORS = ['#000000', '#E69F00', '#56B4E9', '#009E73', '#F0E442', '#0072B2', '#D55E00', '#CC79A7']
+
+
+def get_base_style() -> Dict[str, Any]:
+    """
+    Get base publication-quality style settings.
+
+    Returns
+    -------
+    dict
+        Dictionary of matplotlib rcParams
+    """
+    return {
+        # Figure
+        'figure.dpi': 100,  # Display DPI (changed on save)
+        'figure.facecolor': 'white',
+        'figure.autolayout': False,
+        'figure.constrained_layout.use': True,
+
+        # Font
+        'font.size': 8,
+        'font.family': 'sans-serif',
+        'font.sans-serif': ['Arial', 'Helvetica', 'DejaVu Sans'],
+
+        # Axes
+        'axes.linewidth': 0.5,
+        'axes.labelsize': 9,
+        'axes.titlesize': 9,
+        'axes.labelweight': 'normal',
+        'axes.spines.top': False,
+        'axes.spines.right': False,
+        'axes.spines.left': True,
+        'axes.spines.bottom': True,
+        'axes.edgecolor': 'black',
+        'axes.labelcolor': 'black',
+        'axes.axisbelow': True,
+        'axes.prop_cycle': mpl.cycler(color=OKABE_ITO_COLORS),
+
+        # Grid
+        'axes.grid': False,
+
+        # Ticks
+        'xtick.major.size': 3,
+        'xtick.minor.size': 2,
+        'xtick.major.width': 0.5,
+        'xtick.minor.width': 0.5,
+        'xtick.labelsize': 7,
+        'xtick.direction': 'out',
+        'ytick.major.size': 3,
+        'ytick.minor.size': 2,
+        'ytick.major.width': 0.5,
+        'ytick.minor.width': 0.5,
+        'ytick.labelsize': 7,
+        'ytick.direction': 'out',
+
+        # Lines
+        'lines.linewidth': 1.5,
+        'lines.markersize': 4,
+        'lines.markeredgewidth': 0.5,
+
+        # Legend
+        'legend.fontsize': 7,
+        'legend.frameon': False,
+        'legend.loc': 'best',
+
+        # Savefig
+        'savefig.dpi': 300,
+        'savefig.format': 'pdf',
+        'savefig.bbox': 'tight',
+        'savefig.pad_inches': 0.05,
+        'savefig.transparent': False,
+        'savefig.facecolor': 'white',
+
+        # Image
+        'image.cmap': 'viridis',
+        'image.aspect': 'auto',
+    }
+
+
+def apply_publication_style(style_name: str = 'default') -> None:
+    """
+    Apply a pre-configured publication style.
+
+    Parameters
+    ----------
+    style_name : str, default 'default'
+        Name of the style to apply. Options:
+        - 'default': General publication style
+        - 'nature': Nature journal style
+        - 'science': Science journal style
+        - 'cell': Cell Press style
+        - 'minimal': Minimal clean style
+        - 'presentation': Larger fonts for presentations
+
+    Examples
+    --------
+    >>> apply_publication_style('nature')
+    >>> fig, ax = plt.subplots()
+    >>> ax.plot([1, 2, 3], [1, 4, 9])
+    """
+    base_style = get_base_style()
+
+    # Style-specific modifications
+    if style_name == 'nature':
+        base_style.update({
+            'font.size': 7,
+            'axes.labelsize': 8,
+            'axes.titlesize': 8,
+            'xtick.labelsize': 6,
+            'ytick.labelsize': 6,
+            'legend.fontsize': 6,
+            'savefig.dpi': 600,
+        })
+
+    elif style_name == 'science':
+        base_style.update({
+            'font.size': 7,
+            'axes.labelsize': 8,
+            'xtick.labelsize': 6,
+            'ytick.labelsize': 6,
+            'legend.fontsize': 6,
+            'savefig.dpi': 600,
+        })
+
+    elif style_name == 'cell':
+        base_style.update({
+            'font.size': 8,
+            'axes.labelsize': 9,
+            'xtick.labelsize': 7,
+            'ytick.labelsize': 7,
+            'legend.fontsize': 7,
+            'savefig.dpi': 600,
+        })
+
+    elif style_name == 'minimal':
+        base_style.update({
+            'axes.linewidth': 0.8,
+            'xtick.major.width': 0.8,
+            'ytick.major.width': 0.8,
+            'lines.linewidth': 2,
+        })
+
+    elif style_name == 'presentation':
+        base_style.update({
+            'font.size': 14,
+            'axes.labelsize': 16,
+            'axes.titlesize': 18,
+            'xtick.labelsize': 12,
+            'ytick.labelsize': 12,
+            'legend.fontsize': 12,
+            'axes.linewidth': 1.5,
+            'lines.linewidth': 2.5,
+            'lines.markersize': 8,
+        })
+
+    elif style_name != 'default':
+        print(f"Warning: Style '{style_name}' not recognized. Using 'default'.")
+
+    # Apply the style
+    plt.rcParams.update(base_style)
+    print(f"✓ Applied '{style_name}' publication style")
+
+
+def set_color_palette(palette_name: str = 'okabe_ito') -> None:
+    """
+    Set a colorblind-friendly color palette.
+
+    Parameters
+    ----------
+    palette_name : str, default 'okabe_ito'
+        Name of the palette. Options:
+        - 'okabe_ito': Okabe-Ito palette (8 colors)
+        - 'wong': Wong palette (8 colors)
+        - 'tol_bright': Paul Tol bright palette (7 colors)
+        - 'tol_muted': Paul Tol muted palette (9 colors)
+        - 'tol_high_contrast': Paul Tol high contrast (3 colors)
+
+    Examples
+    --------
+    >>> set_color_palette('tol_muted')
+    >>> fig, ax = plt.subplots()
+    >>> for i in range(5):
+    ...     ax.plot([1, 2, 3], [i, i+1, i+2])
+    """
+    palettes = {
+        'okabe_ito': OKABE_ITO_COLORS,
+        'wong': WONG_COLORS,
+        'tol_bright': TOL_BRIGHT,
+        'tol_muted': TOL_MUTED,
+        'tol_high_contrast': TOL_HIGH_CONTRAST,
+    }
+
+    if palette_name not in palettes:
+        available = ', '.join(palettes.keys())
+        print(f"Warning: Palette '{palette_name}' not found. Available: {available}")
+        palette_name = 'okabe_ito'
+
+    colors = palettes[palette_name]
+    plt.rcParams['axes.prop_cycle'] = plt.cycler(color=colors)
+    print(f"✓ Applied '{palette_name}' color palette ({len(colors)} colors)")
+
+
+def configure_for_journal(journal: str, figure_width: str = 'single') -> None:
+    """
+    Configure matplotlib for a specific journal.
+
+    Parameters
+    ----------
+    journal : str
+        Journal name: 'nature', 'science', 'cell', 'plos', 'acs', 'ieee'
+    figure_width : str, default 'single'
+        Figure width: 'single' or 'double' column
+
+    Examples
+    --------
+    >>> configure_for_journal('nature', figure_width='single')
+    >>> fig, ax = plt.subplots()  # Will have correct size for Nature
+    """
+    journal = journal.lower()
+
+    # Journal specifications
+    journal_configs = {
+        'nature': {
+            'single_width': 89,  # mm
+            'double_width': 183,
+            'style': 'nature',
+        },
+        'science': {
+            'single_width': 55,
+            'double_width': 175,
+            'style': 'science',
+        },
+        'cell': {
+            'single_width': 85,
+            'double_width': 178,
+            'style': 'cell',
+        },
+        'plos': {
+            'single_width': 83,
+            'double_width': 173,
+            'style': 'default',
+        },
+        'acs': {
+            'single_width': 82.5,
+            'double_width': 178,
+            'style': 'default',
+        },
+        'ieee': {
+            'single_width': 89,
+            'double_width': 182,
+            'style': 'default',
+        },
+    }
+
+    if journal not in journal_configs:
+        available = ', '.join(journal_configs.keys())
+        raise ValueError(f"Journal '{journal}' not recognized. Available: {available}")
+
+    config = journal_configs[journal]
+
+    # Apply style
+    apply_publication_style(config['style'])
+
+    # Set default figure size
+    width_mm = config['single_width'] if figure_width == 'single' else config['double_width']
+    width_inches = width_mm / 25.4
+    plt.rcParams['figure.figsize'] = (width_inches, width_inches * 0.75)  # 4:3 aspect ratio
+
+    print(f"✓ Configured for {journal.upper()} ({figure_width} column: {width_mm} mm)")
+
+
+def create_style_template(output_file: str = 'publication.mplstyle') -> None:
+    """
+    Create a matplotlib style file that can be used with plt.style.use().
+
+    Parameters
+    ----------
+    output_file : str, default 'publication.mplstyle'
+        Output filename for the style file
+
+    Examples
+    --------
+    >>> create_style_template('my_style.mplstyle')
+    >>> plt.style.use('my_style.mplstyle')
+    """
+    style = get_base_style()
+
+    with open(output_file, 'w') as f:
+        f.write("# Publication-quality matplotlib style\n")
+        f.write("# Usage: plt.style.use('publication.mplstyle')\n\n")
+
+        for key, value in style.items():
+            if isinstance(value, mpl.cycler):
+                # Handle cycler specially
+                colors = [c['color'] for c in value]
+                f.write(f"axes.prop_cycle : cycler('color', {colors})\n")
+            else:
+                f.write(f"{key} : {value}\n")
+
+    print(f"✓ Created style template: {output_file}")
+    print(f"  Use with: plt.style.use('{output_file}')")
+
+
+def show_color_palettes() -> None:
+    """
+    Display available color palettes for visual inspection.
+    """
+    palettes = {
+        'Okabe-Ito': OKABE_ITO_COLORS,
+        'Wong': WONG_COLORS,
+        'Tol Bright': TOL_BRIGHT,
+        'Tol Muted': TOL_MUTED,
+        'Tol High Contrast': TOL_HIGH_CONTRAST,
+    }
+
+    fig, axes = plt.subplots(len(palettes), 1, figsize=(8, len(palettes) * 0.5))
+
+    for ax, (name, colors) in zip(axes, palettes.items()):
+        ax.set_xlim(0, len(colors))
+        ax.set_ylim(0, 1)
+        ax.set_yticks([])
+        ax.set_xticks([])
+        ax.set_ylabel(name, fontsize=10)
+
+        for i, color in enumerate(colors):
+            ax.add_patch(plt.Rectangle((i, 0), 1, 1, facecolor=color, edgecolor='black', linewidth=0.5))
+            # Add hex code
+            ax.text(i + 0.5, 0.5, color, ha='center', va='center',
+                   fontsize=7, color='white' if i >= len(colors) - 1 else 'black')
+
+    fig.suptitle('Colorblind-Friendly Palettes', fontsize=12, fontweight='bold')
+    plt.tight_layout()
+    plt.show()
+
+
+def reset_to_default() -> None:
+    """
+    Reset matplotlib to default settings.
+    """
+    mpl.rcdefaults()
+    print("✓ Reset to matplotlib defaults")
+
+
+if __name__ == "__main__":
+    print("Matplotlib Style Presets for Scientific Figures")
+    print("=" * 50)
+
+    # Show available styles
+    print("\nAvailable publication styles:")
+    print("  - default")
+    print("  - nature")
+    print("  - science")
+    print("  - cell")
+    print("  - minimal")
+    print("  - presentation")
+
+    print("\nAvailable color palettes:")
+    print("  - okabe_ito (recommended)")
+    print("  - wong")
+    print("  - tol_bright")
+    print("  - tol_muted")
+    print("  - tol_high_contrast")
+
+    print("\nExample usage:")
+    print("  from style_presets import apply_publication_style, set_color_palette")
+    print("  apply_publication_style('nature')")
+    print("  set_color_palette('okabe_ito')")
+
+    # Create example figure
+    print("\nGenerating example figure with 'default' style...")
+    apply_publication_style('default')
+
+    fig, ax = plt.subplots(figsize=(3.5, 2.5))
+    for i in range(5):
+        ax.plot([1, 2, 3, 4], [i, i+1, i+0.5, i+2], marker='o', label=f'Series {i+1}')
+    ax.set_xlabel('Time (hours)')
+    ax.set_ylabel('Response (AU)')
+    ax.legend()
+    fig.suptitle('Example with Publication Style')
+    plt.tight_layout()
+    plt.show()
+
+    # Show color palettes
+    print("\nDisplaying color palettes...")
+    show_color_palettes()