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Zhongwei Li
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skills/scientific-visualization/scripts/figure_export.py
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343
skills/scientific-visualization/scripts/figure_export.py
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#!/usr/bin/env python3
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"""
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Figure Export Utilities for Publication-Ready Scientific Figures
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This module provides utilities to export matplotlib figures in publication-ready
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formats with appropriate settings for various journals.
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"""
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import matplotlib.pyplot as plt
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from pathlib import Path
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from typing import List, Optional, Union
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def save_publication_figure(
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fig: plt.Figure,
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filename: Union[str, Path],
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formats: List[str] = ['pdf', 'png'],
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dpi: int = 300,
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transparent: bool = False,
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bbox_inches: str = 'tight',
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pad_inches: float = 0.1,
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facecolor: str = 'white',
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**kwargs
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) -> List[Path]:
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"""
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Save a matplotlib figure in multiple formats with publication-quality settings.
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Parameters
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----------
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fig : matplotlib.figure.Figure
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The figure to save
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filename : str or Path
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Base filename (without extension)
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formats : list of str, default ['pdf', 'png']
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List of file formats to save. Options: 'pdf', 'png', 'eps', 'svg', 'tiff'
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dpi : int, default 300
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Resolution for raster formats (png, tiff). 300 DPI is minimum for most journals
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transparent : bool, default False
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If True, save with transparent background
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bbox_inches : str, default 'tight'
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Bounding box specification. 'tight' removes excess whitespace
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pad_inches : float, default 0.1
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Padding around the figure when bbox_inches='tight'
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facecolor : str, default 'white'
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Background color (ignored if transparent=True)
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**kwargs
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Additional keyword arguments passed to fig.savefig()
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Returns
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-------
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list of Path
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List of paths to saved files
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Examples
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--------
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>>> fig, ax = plt.subplots()
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>>> ax.plot([1, 2, 3], [1, 4, 9])
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>>> save_publication_figure(fig, 'my_plot', formats=['pdf', 'png'], dpi=600)
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['my_plot.pdf', 'my_plot.png']
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"""
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filename = Path(filename)
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base_name = filename.stem
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output_dir = filename.parent if filename.parent.exists() else Path.cwd()
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saved_files = []
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for fmt in formats:
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output_file = output_dir / f"{base_name}.{fmt}"
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# Set format-specific parameters
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save_kwargs = {
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'dpi': dpi,
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'bbox_inches': bbox_inches,
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'pad_inches': pad_inches,
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'facecolor': facecolor if not transparent else 'none',
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'edgecolor': 'none',
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'transparent': transparent,
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'format': fmt,
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}
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# Update with user-provided kwargs
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save_kwargs.update(kwargs)
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# Adjust DPI for vector formats (DPI less relevant)
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if fmt in ['pdf', 'eps', 'svg']:
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save_kwargs['dpi'] = min(dpi, 300) # Lower DPI for embedded rasters in vector
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try:
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fig.savefig(output_file, **save_kwargs)
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saved_files.append(output_file)
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print(f"✓ Saved: {output_file}")
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except Exception as e:
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print(f"✗ Failed to save {output_file}: {e}")
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return saved_files
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def save_for_journal(
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fig: plt.Figure,
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filename: Union[str, Path],
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journal: str,
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figure_type: str = 'combination'
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) -> List[Path]:
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"""
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Save figure with journal-specific requirements.
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Parameters
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----------
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fig : matplotlib.figure.Figure
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The figure to save
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filename : str or Path
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Base filename (without extension)
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journal : str
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Journal name. Options: 'nature', 'science', 'cell', 'plos', 'acs', 'ieee'
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figure_type : str, default 'combination'
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Type of figure. Options: 'line_art', 'photo', 'combination'
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Returns
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-------
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list of Path
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List of paths to saved files
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Examples
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--------
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>>> fig, ax = plt.subplots()
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>>> ax.plot([1, 2, 3], [1, 4, 9])
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>>> save_for_journal(fig, 'figure1', journal='nature', figure_type='line_art')
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"""
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journal = journal.lower()
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# Define journal-specific requirements
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journal_specs = {
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'nature': {
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'line_art': {'formats': ['pdf', 'eps'], 'dpi': 1000},
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'photo': {'formats': ['tiff'], 'dpi': 300},
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'combination': {'formats': ['pdf'], 'dpi': 600},
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},
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'science': {
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'line_art': {'formats': ['eps', 'pdf'], 'dpi': 1000},
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'photo': {'formats': ['tiff'], 'dpi': 300},
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'combination': {'formats': ['eps'], 'dpi': 600},
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},
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'cell': {
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'line_art': {'formats': ['pdf', 'eps'], 'dpi': 1000},
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'photo': {'formats': ['tiff'], 'dpi': 300},
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'combination': {'formats': ['pdf'], 'dpi': 600},
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},
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'plos': {
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'line_art': {'formats': ['pdf', 'eps'], 'dpi': 600},
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'photo': {'formats': ['tiff', 'png'], 'dpi': 300},
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'combination': {'formats': ['tiff'], 'dpi': 300},
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},
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'acs': {
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'line_art': {'formats': ['tiff', 'pdf'], 'dpi': 600},
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'photo': {'formats': ['tiff'], 'dpi': 300},
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'combination': {'formats': ['tiff'], 'dpi': 600},
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},
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'ieee': {
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'line_art': {'formats': ['pdf', 'eps'], 'dpi': 600},
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'photo': {'formats': ['tiff'], 'dpi': 300},
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'combination': {'formats': ['pdf'], 'dpi': 300},
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},
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}
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if journal not in journal_specs:
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available = ', '.join(journal_specs.keys())
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raise ValueError(f"Journal '{journal}' not recognized. Available: {available}")
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if figure_type not in journal_specs[journal]:
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available = ', '.join(journal_specs[journal].keys())
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raise ValueError(f"Figure type '{figure_type}' not valid. Available: {available}")
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specs = journal_specs[journal][figure_type]
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print(f"Saving for {journal.upper()} ({figure_type}):")
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print(f" Formats: {', '.join(specs['formats'])}")
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print(f" DPI: {specs['dpi']}")
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return save_publication_figure(
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fig=fig,
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filename=filename,
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formats=specs['formats'],
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dpi=specs['dpi']
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)
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def check_figure_size(fig: plt.Figure, journal: str = 'nature') -> dict:
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"""
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Check if figure dimensions are appropriate for journal requirements.
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Parameters
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----------
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fig : matplotlib.figure.Figure
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The figure to check
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journal : str, default 'nature'
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Journal name
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Returns
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-------
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dict
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Dictionary with figure dimensions and compliance status
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Examples
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--------
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>>> fig = plt.figure(figsize=(3.5, 3))
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>>> info = check_figure_size(fig, journal='nature')
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>>> print(info)
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"""
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journal = journal.lower()
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# Get figure dimensions in inches
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width_inches, height_inches = fig.get_size_inches()
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width_mm = width_inches * 25.4
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height_mm = height_inches * 25.4
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# Journal specifications (widths in mm)
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specs = {
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'nature': {'single': 89, 'double': 183, 'max_height': 247},
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'science': {'single': 55, 'double': 175, 'max_height': 233},
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'cell': {'single': 85, 'double': 178, 'max_height': 230},
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'plos': {'single': 83, 'double': 173, 'max_height': 233},
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'acs': {'single': 82.5, 'double': 178, 'max_height': 247},
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}
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if journal not in specs:
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journal_spec = specs['nature']
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print(f"Warning: Journal '{journal}' not found, using Nature specifications")
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else:
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journal_spec = specs[journal]
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# Determine column type
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column_type = None
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width_ok = False
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tolerance = 5 # mm tolerance
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if abs(width_mm - journal_spec['single']) < tolerance:
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column_type = 'single'
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width_ok = True
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elif abs(width_mm - journal_spec['double']) < tolerance:
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column_type = 'double'
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width_ok = True
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height_ok = height_mm <= journal_spec['max_height']
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result = {
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'width_inches': width_inches,
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'height_inches': height_inches,
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'width_mm': width_mm,
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'height_mm': height_mm,
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'journal': journal,
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'column_type': column_type,
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'width_ok': width_ok,
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'height_ok': height_ok,
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'compliant': width_ok and height_ok,
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'recommendations': {
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'single_column_mm': journal_spec['single'],
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'double_column_mm': journal_spec['double'],
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'max_height_mm': journal_spec['max_height'],
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}
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}
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# Print report
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print(f"\n{'='*60}")
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print(f"Figure Size Check for {journal.upper()}")
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print(f"{'='*60}")
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print(f"Current size: {width_mm:.1f} × {height_mm:.1f} mm")
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print(f" ({width_inches:.2f} × {height_inches:.2f} inches)")
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print(f"\n{journal.upper()} specifications:")
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print(f" Single column: {journal_spec['single']} mm")
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print(f" Double column: {journal_spec['double']} mm")
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print(f" Max height: {journal_spec['max_height']} mm")
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print(f"\nCompliance:")
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print(f" Width: {'✓ OK' if width_ok else '✗ Non-standard'} ({column_type or 'custom'})")
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print(f" Height: {'✓ OK' if height_ok else '✗ Too tall'}")
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print(f" Overall: {'✓ COMPLIANT' if result['compliant'] else '✗ NEEDS ADJUSTMENT'}")
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print(f"{'='*60}\n")
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return result
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def verify_font_embedding(pdf_path: Union[str, Path]) -> bool:
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"""
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Check if fonts are embedded in a PDF file.
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Note: This requires PyPDF2 or a similar library to be installed.
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Parameters
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----------
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pdf_path : str or Path
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Path to PDF file
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Returns
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-------
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bool
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True if fonts are embedded, False otherwise
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"""
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try:
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from PyPDF2 import PdfReader
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except ImportError:
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print("Warning: PyPDF2 not installed. Cannot verify font embedding.")
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print("Install with: pip install PyPDF2")
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return None
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pdf_path = Path(pdf_path)
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try:
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reader = PdfReader(pdf_path)
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# This is a simplified check; full verification is complex
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print(f"PDF has {len(reader.pages)} page(s)")
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print("Note: Full font embedding verification requires detailed PDF inspection.")
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return True
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except Exception as e:
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print(f"Error reading PDF: {e}")
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return False
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if __name__ == "__main__":
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# Example usage
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import numpy as np
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# Create example figure
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fig, ax = plt.subplots(figsize=(3.5, 2.5))
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x = np.linspace(0, 10, 100)
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ax.plot(x, np.sin(x), label='sin(x)')
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ax.plot(x, np.cos(x), label='cos(x)')
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ax.set_xlabel('x')
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ax.set_ylabel('y')
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ax.legend()
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ax.spines['top'].set_visible(False)
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ax.spines['right'].set_visible(False)
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# Check size
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check_figure_size(fig, journal='nature')
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# Save in multiple formats
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print("\nSaving figure...")
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save_publication_figure(fig, 'example_figure', formats=['pdf', 'png'], dpi=300)
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# Save with journal-specific requirements
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print("\nSaving for Nature...")
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save_for_journal(fig, 'example_figure_nature', journal='nature', figure_type='line_art')
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plt.close(fig)
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