Align all paper example figures with MATLAB layouts and styles#76
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iahncajigas merged 12 commits intomainfrom Mar 24, 2026
Merged
Align all paper example figures with MATLAB layouts and styles#76iahncajigas merged 12 commits intomainfrom
iahncajigas merged 12 commits intomainfrom
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Part B (Figures 3-4): - Replace sinusoidal trajectory with minimum-jerk reaching dynamics (cosine acceleration toward target), matching MATLAB exactly - Fix encoding parameters: delta=0.001, mu=log(10*delta)+randn, beta=10*(rand-0.5) uniform velocity tuning - Figure 3: 4x2 layout with reach path, pos/vel traces, raster, CIF - Figure 4: overlaid decoded trajectories (20 runs, blue=goal, green=free) Part C (Figures 5-6): - Load 6-state fixture (paperHybridFilterExample.mat) with 2D hold and 6D reach modes, matching MATLAB's different-dimension-per-mode hybrid filter architecture - Figure 5: 4x2 layout with reach path, pos/vel traces, raster, discrete state (N/M) - Figure 6: 4x3 layout with state estimation, P(M|data), 2D decoded path, per-component traces — averaged over 20 simulations with both goal-directed and free hybrid decoding Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The likelihood computation in PPHybridFilterLinear and PPHybridFilter used sqrt(det(W_u)) / max(sqrt(det(W_p)), 1e-15) which catastrophically fails for ≥6-D states: with eigenvalues ~1e-10, det ≈ 1e-46 and sqrt(det) ≈ 1e-23 — far below the 1e-15 floor — collapsing the reach model likelihood to zero permanently. Replace with np.linalg.slogdet() log-space computation that matches MATLAB's raw det ratio while avoiding overflow/underflow. Verified: 100% discrete-state agreement with MATLAB (fixed) on the paperHybridFilterExample fixture for both free and goal-directed cases. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Regenerated all 24 figures across 5 paper examples with latest code - Re-executed all 29 help notebooks (helpfiles) with fresh outputs - Added example figure exports to examples/paper/figures/ (new) - Updated docs/figures/ gallery with cleaned manifest-matching figures - Fixed test_network_tutorial_builder to strip execution metadata Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Documentation links now point to actual Sphinx-generated paths (help/index.html, help/paper_overview.html, etc.) instead of non-existent flat filenames (NeuralSpikeAnalysis_top.html, etc.) - Fix parity report link: parity/parity_report.md -> parity/report.md - Add parity dashboard and API reference links - Remove stale DocumentationSetup.md source page reference Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…, and styles
Cross-referenced all MATLAB example scripts against Python to match subplot
grids, axis labels, title text, font properties (Arial, bold, 12-16pt),
line widths, marker styles, tick formatting, and legend content.
Key changes per example:
- Ex01: Replace plotResults() with explicit 2x2 grid matching MATLAB (raster,
InvGausTrans, KSPlot, lambda); add red epoch lines and dual-lambda plot
- Ex02: Match MATLAB 16pt titles, axis tick formatting, suppress top-panel
x-labels, use "Displacement Velocity" title, hide coefficient legend
- Ex03: Match MATLAB CIF title wording, mesh wireframe appearance with
edgecolor/alpha, figsize (14,9) for surface plots
- Ex04: Add axis('square'), XTick/YTick [-1:0.5:1], Cell# titles, legend on
subplot 4, remove subplot borders for place fields, sgtitle format
- Ex05: Match figsize (14,9), linewidth=4 for decoded traces, 18pt title,
show all cells in hybrid raster, suppress raster x-labels
Regenerated all 25 figures in both examples/paper/figures/ and docs/figures/.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The test_readme_links_to_help_navigation_pages test expects all five MATLAB-style navigation pages to be linked in the README. The DocumentationSetup.md page existed in docs/ but was not listed in the Source pages section. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Figure fixes (all 5 examples): - Ex01 Fig3: Epoch lines bounded to [0,1] instead of full y-axis (axvline → plot) - Ex02 Fig1: Add axis linewidth=1 on subplots 2-3 (matching MATLAB set(gca,'LineWidth',1)) - Ex03 Fig3: CIF heatmap uses jet colormap (matching MATLAB imagesc default) - Ex03 Fig5: plot_wireframe instead of plot_surface (matching MATLAB mesh()) - Ex03 Fig2: PSTH/GLM z-order swapped to match MATLAB (GLM drawn before PSTH markers) - Ex03 Fig6: Significance markers markersize 3→6; axis label positions moved to top/right - Ex04 Fig1: Aspect ratio 12×10→14×9 (matching MATLAB 1400×900) - Ex04 Fig2: Figure height 5→9 inches - Ex04 Figs3-6: Fixed heatmap heights to 14×9 instead of scaling with row count - Ex04 Fig7: plot_wireframe instead of plot_surface with Line2D legend entries - Ex05: Raster markersize 2→4; added missing "Stimulus" ylabel on Fig2 README restructured to match MATLAB README flow: - Added subtitle "Neural Spike Train Analysis Toolbox for Python" - Moved CI badge to after title - Removed broken pages.yml badge (no workflow exists) - Consolidated install/data/setup into single "How to install nSTAT" section - Merged License, Cite, Data into single section - Added PyPI install one-liner before lab websites Docs: - Added CITATION.cff mirroring MATLAB repo - Regenerated all 25 paper-example figures Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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- example03: Add missing K_mesh/T_mesh meshgrid for Figure 5 wireframe surfaces (NameError at runtime) - example05: Add missing _simulate_binomial_spikes() helper that computes CIF from state/coefficients then draws spikes (NameError in Parts B/C) - example05: Fix x_true → stimSignal reference in Figure 2 plotting - example05: Remove dead "setup" key from _load_hybrid_fixture() return - Regenerate all affected figures for examples 03 and 05 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- AnalysisExamples2.ipynb: getCoeffs() returns (coeffs, labels, SE) tuple, need [0] to extract coefficient array for subtraction - StimulusDecode2D.ipynb: parity note said 'exact' but parity_notes.yml says 'high_fidelity'; align notebook to YAML Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Trim algorithm-specific details from overview (SSGLM, UKF, PPAF, PPHF) to match MATLAB's general-purpose intro paragraphs - Move Plot Style into Paper Examples section (matching MATLAB placement) - Add Quickstart block (matching MATLAB's run_all_checks one-liner) - Simplify Documentation to single GitHub Pages URL (matching MATLAB) - Remove standalone Supplementary Examples and Developer Notes sections - Trim Toolbox Map to 5 bullets matching MATLAB's structure - Consolidate citation/license into flowing prose (matching MATLAB) - Update test_docs_surface.py: replace per-page README link test with GitHub Pages site link test (mirrors MATLAB README structure) - Fix StimulusDecode2D.ipynb parity note remaining_differences to match parity_notes.yml Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- paper_gallery.py: Output "## Paper Examples (Self-Contained)" heading to match MATLAB's "Paper Examples (Self-Contained)" section structure - paper_gallery.py: Remove Supplementary Examples from generated output (MATLAB README has no equivalent section) - paper_gallery.py: Update README delimiters for new section headings - test_docs_surface.py: Replace per-page README link tests with GitHub Pages URL and PaperOverview link tests (matching MATLAB's single-URL documentation reference) - StimulusDecode2D.ipynb: Align parity note with parity_notes.yml Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…le04 figures - test_paper_gallery_docs.py: Update delimiter from "## Examples" to "## Paper Examples (Self-Contained)" / "Plot style policy:" - test_readme_examples_catalog.py: Remove Supplementary Examples test (section removed from README for MATLAB parity); update block extractor - test_readme_nstatpaperexamples.py: Update regex for new section heading - Regenerate example04 figures at full DPI=250 resolution (3500x2250) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
examples/paper/figures/anddocs/figures/Per-example changes
plotResults()with explicit 2×2 grid matching MATLAB (raster + InvGausTrans + KSPlot + lambda); added red epoch lines and dual-lambda overlay in Figure 3axis('square'), XTick/YTick[-1:0.5:1],Cell#titles, legend on subplot 4, removed subplot borders for place fields, matchedsgtitleformatTest plan
--export-figurespytest tests/ -k paper)🤖 Generated with Claude Code