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rseng-scientific-visualization

Covers visualization of scientific data beyond publication figures: 3D and volumetric rendering with ParaView and VTK, scripted and reproducible visualization pipelines, state files and Python trace for repeatability, in-situ visualization of running simulations, web-delivered interactive 3D (trame-style apps), and choosing honest colormaps and representations for spatial data. Use when the user works with 3D, volumetric, mesh or simulation output data, mentions ParaView, VTK or interactive 3D viewers, needs a visualization others can regenerate, or wants to inspect large simulation results.

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fdiblen/rseng-agent-skills24 stars(GitHub 24 + cccskills 0)

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SKILL.md (original)

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Scientific visualization

Scientific visualization turns meshes, fields and volumes into understanding - and, done as engineering rather than clicking, into REPRODUCIBLE artifacts: a figure or animation anyone can regenerate from data plus a script. The reference stack is VTK (the rendering and data-processing library) and ParaView (the application built on it, scriptable in Python); the practices below outlast any one tool.

Reproducibility first

An interactively composed visualization is a dead end the moment it is needed again. Make visualizations regenerable:

  • Script the pipeline: ParaView's Python tracing records interactive work as a pvpython script - clean it, parameterize the input path, and commit it next to the analysis code (rseng-version-control-review).
  • State files capture a full session as a restorable artifact; scripts beat state files for review and parameterization, state files beat nothing.
  • Treat visualization scripts as code: inputs and camera/colormap parameters in configuration, outputs written to a results directory, runnable headless in the pipeline (rseng-workflows) so figures regenerate when data changes.
  • Record the tool version with the output - renderers evolve, and a pinned environment (rseng-reproducible-environments) keeps animations regenerable years later.

Honest representation

  • Colormaps: perceptually uniform by default (viridis-class); rainbow/jet-class maps create false boundaries and mislead - flag them on sight. Diverging maps only for data with a meaningful center; always show the colorbar with units (rseng-scientific-file-formats' unit discipline pays off here).
  • Respect the data's structure: do not interpolate across discontinuities, do not volume-render categorical data, state isovalue choices - an isosurface at an arbitrary threshold is an editorial decision and should be a labeled parameter.
  • Accessibility applies: colorblind-safe maps, readable annotation sizes in videos and figures (rseng-ux-accessibility).

Scale: large data and in-situ

  • Larger-than-memory results: use parallel/distributed rendering (pvserver) or level-of-detail decimation for interaction, full resolution for final renders; chunk-friendly file layouts (rseng-scientific-file-formats) decide how painful this is.
  • In-situ visualization (ParaView Catalyst-style) renders DURING the simulation instead of writing everything to disk - the escape hatch when output volume makes post-hoc analysis impossible; it changes I/O planning (rseng-hpc-computing).
  • Batch renders of animations belong on the cluster as jobs, not on laptops overnight (rseng-hpc-computing).

Sharing and interaction

  • Web delivery lets collaborators explore 3D results without installing anything: trame-style Python apps expose a VTK/ParaView pipeline in the browser; a hosted viewer is a research service with operational needs when it outlives a demo.
  • For talks and papers, render key frames as static figures with the same scripted pipeline - one source of truth for interactive and print outputs (rseng-science-communication for the framing).

Working with this skill

This skill is source-independent: its authority is the VTK and ParaView documentation linked below.

Learn more (verified):

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Related skills

Check whether any of these applies before moving on:

  • rseng-hpc-computing - parallel rendering and in-situ output
  • rseng-reproducibility - regenerable figures from scripts
  • rseng-science-communication - framing figures for talks and papers
  • rseng-scientific-file-formats - mesh and volume data layouts
  • rseng-ux-accessibility - colorblind-safe maps and annotations
  • rseng-workflows - figures regenerate inside pipelines
<!-- related-skills:end -->

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