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The Optics Project on the Web (WebTOP) is a 3D, interactive computer graphics system that visualizes optical phenomena. Its purpose is to help instructors teach and students learn about optics. It is a platform independent Java application that uses X3D.
Easy-to-learn interactive 2d plot program. Can overlay images, xy-data, and mathematical functions. Function parameters can be tuned with sliders; functions can also be automatically fitted to data. Written in Python, cross-platform, but currently broken
Vistools is a set of tools to easily visualize some scientific data, without need to learn difficult API, so you can see your 3d results very quickly. Also some sci tools for which we made it, including vector field tracing and simple optimization.