3D axis orientation

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I've see a few different approaches on axis-orientation in R3, and I'm currently in the process of performing operations in this space specifically for rendering. The problem is that I'm running into issues where one of the axes is the negative counter-part to what is expected. I suspect the issue lies in how I am picturing the axis orientation in my head. So the question is, what is the most accepted version of coordinate axes in 3D space (e.g. z-axis for "altitude"?) ? Is there a specific reason why this method is better than other methods? Does the cross product of 2 specific axes always have to output the 3rd axis or its negative?