When is it Legal to Reverse Engineer Software?

A not-so Anonymous Coward asks: "I'm the lead developer of SciGraphica, an open source application for scientific graphics that runs under Linux, and is based on Microcal Origin, the commercial application for Windows. When we contacted this company, they let us know that a port for Linux or other operating systems was not in their plans, and that they were not willing to make their proprietary file format available. However, we realized that it is in fact easy to reverse engineer to create a filter that would allow our program to read Origin files. Are we walking into a case of patent infringement, or this is a legitimate solution? If this is problematic, is there a way to allow people to legally have access to the filter?"