figure-generator

Figure Generator

Overview

This skill runs after the writer skill has produced LaTeX prose. It reads .tex files, finds figure placeholders, and generates actual figures where possible. It replaces \figurePlaceholder{...} blocks with \includegraphics{...} pointing to generated output.

When to Use This Skill

• After writer has produced .tex files containing figure placeholders
• When updating figures after data or methods changes
• When regenerating specific figures

Plot Defaults File

Before generating any figures, check for figures/plot_defaults.py in the document directory. If it does not exist, create it. This file defines all shared styling for consistency across the entire thesis.

# figures/plot_defaults.py
# Shared matplotlib defaults for all thesis figures.
# Edit this file to change styling globally.

import matplotlib.pyplot as plt
import matplotlib as mpl

# --- Colour palette ---
COLOURS = {
    'primary': '#1f77b4',
    'secondary': '#ff7f0e',
    'tertiary': '#2ca02c',
    'quaternary': '#d62728',
    'grey': '#7f7f7f',
    'light_grey': '#c7c7c7',
}
COLOUR_CYCLE = [COLOURS['primary'], COLOURS['secondary'], COLOURS['tertiary'],
                COLOURS['quaternary'], COLOURS['grey']]

# --- Figure sizes (inches) ---
SINGLE_COL = (6.5, 4.0)
DOUBLE_COL = (6.5, 3.0)    # wide but short
HALF_COL = (3.15, 3.0)     # for subfigures

# --- Font and text ---
FONT_FAMILY = 'serif'
FONT_SIZE = 10
LABEL_SIZE = 11
TICK_SIZE = 9
LEGEND_SIZE = 9

# --- Line and marker ---
LINE_WIDTH = 1.5
MARKER_SIZE = 4

# --- Export ---
DPI = 300
FORMATS = ['pdf', 'png']  # pdf for LaTeX, png for preview


def apply():
    """Apply thesis defaults to matplotlib rcParams."""
    mpl.rcParams.update({
        'font.family': FONT_FAMILY,
        'font.size': FONT_SIZE,
        'axes.labelsize': LABEL_SIZE,
        'axes.titlesize': LABEL_SIZE,
        'xtick.labelsize': TICK_SIZE,
        'ytick.labelsize': TICK_SIZE,
        'legend.fontsize': LEGEND_SIZE,
        'figure.figsize': SINGLE_COL,
        'figure.dpi': DPI,
        'savefig.dpi': DPI,
        'savefig.bbox': 'tight',
        'lines.linewidth': LINE_WIDTH,
        'lines.markersize': MARKER_SIZE,
        'axes.prop_cycle': mpl.cycler(color=COLOUR_CYCLE),
    })


def savefig(fig, path_stem):
    """Save figure in all configured formats."""
    for fmt in FORMATS:
        fig.savefig(f'{path_stem}.{fmt}', dpi=DPI, bbox_inches='tight')

Every generated script must:

1. import plot_defaults; plot_defaults.apply() at the top
2. Use plot_defaults.savefig(fig, path) to export
3. Reference plot_defaults.COLOURS, plot_defaults.SINGLE_COL, etc. for sizing and colours

If plot_defaults.py already exists, read it and respect the author's customisations. Only add missing keys — never overwrite existing choices.

Figure Categories

1. Data Plots (auto-generate)

For placeholders that specify data sources, generate Python scripts using matplotlib:

Input (from placeholder):

• Data source path (CSV, HDF5, or reference to source code that produces data)
• Plot type (time series, scatter, bar chart, box plot, Bland-Altman, etc.)
• Axes labels and units
• Key features to highlight

Output:

• Python script in figures/scripts/ that reads data and produces the plot
• Generated figure in figures/ (PDF and PNG)
• Updated .tex with \includegraphics replacing the placeholder

Script requirements:

• Self-contained: runs independently with python script.py
• Imports and applies plot_defaults for consistent styling
• Uses matplotlib only (not seaborn)
• Outputs both PDF (for LaTeX) and PNG (for preview)

2. Simple Schematics (auto-generate)

For block diagrams, system architectures, signal processing pipelines:

Approach: Generate using TikZ directly in LaTeX, or Python (matplotlib/networkx) for more complex diagrams.

Types:

• Block diagrams of systems/methods
• Signal processing pipelines
• Simple circuit representations
• Algorithm flowcharts
• Data flow diagrams

3. Complex/Custom Figures (flag for user)

Some figures cannot be auto-generated:

• Photographs or microscopy images
• Figures requiring the author's unpublished data in inaccessible formats
• Highly specialised domain diagrams
• Figures requiring specific artistic choices

Action: Keep the placeholder but add a % TODO: MANUAL FIGURE REQUIRED comment explaining what's needed and why it couldn't be auto-generated.

Workflow

1. Check defaults: Read or create figures/plot_defaults.py
2. Scan: Read .tex file(s), find all figure placeholder blocks
3. Classify: For each placeholder, determine category (data plot / schematic / complex)
4. Generate: For auto-generatable figures: a. Create Python script (importing plot_defaults) or TikZ code b. Run script to produce figure file c. Replace placeholder with \includegraphics
5. Flag: For complex figures, add TODO comments
6. Report: Summary of what was generated, what was flagged, any issues

LaTeX Integration

Replace:

\begin{figure}[tb]
\centering
\fbox{\parbox{0.8\textwidth}{
\textbf{FIGURE PLACEHOLDER}\\[1em]
...
}}
\caption{Caption text.}
\label{fig:label}
\end{figure}

With:

\begin{figure}[tb]
\centering
\includegraphics[width=\columnwidth]{figures/fig_label}
\caption{Caption text.}
\label{fig:label}
\end{figure}

What This Skill Does NOT Do

• Does not change prose content
• Does not add or remove figures beyond what the plan specifies
• Does not modify captions (preserves writer's captions)
• Does not change figure labels or cross-references

Integration

• Receives from: writer skill (.tex files with figure placeholders)
• Reads: Data files referenced in placeholders, source code for data generation
• Maintains: figures/plot_defaults.py (shared styling for all thesis figures)
• Produces: Figure files in figures/, Python scripts in figures/scripts/, updated .tex files
• Hands off to: formatter skill for final LaTeX polish