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The above bush is made of many initially individual images on planes, one per plane (leafs). Then joined into one mesh. This mesh uses 2 materials. But now I need to replace all these planes with one mesh (which I already made with the Re-mesh modifier, and lots of cleaning). At first I thought I could bake all those planes into one texture to then just apply it to the other single mesh. But after baking I can see it is only using one of the many planes, hence the result is one big leaf in my baked image Any ideas?

Feel free to inspect the blend enter image description here

Thanks guys,

DPC

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Quick mapping (sloppy) of your image on single sphere mesh on the left to simulate your starting point. Middle image is placement of the two participants of the bake. Then baked onto another final mesh on the right side. The 3 images are different stages of the baking process. The created texture has black background which becomes transparent via color ramp and transparent shader. I nested the hemisphere askew to increase readability. All the hemisphere shapes below are a single mesh. Your are seeing objects below with transparency so you may need more time to get the orientation of the object. I may correct this.

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Created texture with black on left. Mapped texture with black. Objects baked in alignment. Below.

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Two alternatives.

    1. Consider Baking in Cycles Render or Blender Render. You will use a new texture to record the color reflection of one source mesh to the other target mesh. Your finished original bushy mesh can be illuminated or set to emission material. We assume your shapes are roughly hemispheres. Hemisphere is sphere cut in half. The target mesh is hemisphere with reflective surface. Original mesh in placed over the reflective target. Bake target mesh. See video references for detailed instruction on baking in cycles render or blender render.
    1. Consider creating a regular rectangular tile of leaves texture, which is expected to be modest work. Leaves in this texture can all be same size. New mesh is cylinder. UV Map cylinder to leaves texture. Leaves appear all same size as in the soup can model. Use proportional editing to reshape cylinder in to hemisphere. In this scenario your original bushy collection of meshes is discarded completely... rather I mean ... placed gently in the experience bin.

Abbreviated Picture Notes Blender Cycles Texture Baking Setup

In the following the red object is your texture object with emission material.

Red emission object is next to green reflective object follows

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Bake Result is the New texture follows

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Texture placed back on green inner object and rendered follows

Original Red object has been set to No Render.

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