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Cycles vs. Blender Internal Texture Baking result

I am trying to write a command-line script that bakes vertex colors from one object to a UV-map on a new object that has been remeshed and smart-projected. I have gotten the code working using Cycles, but I find that the output texture looks a lot worse than when I bake the texture manually using the Blender internal renderer.

I am wondering if there is some setting within Cycles that could be resulting in the "splotchy", inaccurate texture in the image I have attached, or if there is a good reference or example for a baking script working with the Blender internal render. Based on this post it seems like a lot of GUI navigation as opposed to just setting up nodes using Cycles.

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    $\begingroup$ Hi, could you post your images inline? There should be an image icon if you press edit. You can use that to select your image and it will then be posted inside the page instead of in your dropbox. Thanks :) $\endgroup$ Commented Aug 24, 2015 at 0:02
  • $\begingroup$ Ah, thanks. The image is now embedded above. $\endgroup$
    – Mark C.
    Commented Aug 24, 2015 at 0:48
  • $\begingroup$ What bake settings are you using? $\endgroup$
    – sambler
    Commented Aug 24, 2015 at 14:31
  • $\begingroup$ Samples is set to 24, I've been adjusting the margin between 0 and 16 px thinking that this would be the issue, but I think that the texture bleeding seems to happen regardless. $\endgroup$
    – Mark C.
    Commented Aug 24, 2015 at 19:55
  • $\begingroup$ Sorry for not knowing a solution, but the Cycles looks quite artistically interesting. Maybe keep a copy of the setup for other occasions? Question: Is the result any different if you do it in GUI instead of by script? $\endgroup$
    – CodeManX
    Commented Aug 24, 2015 at 20:01

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