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