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Having read these docs, im still somewhat confused on generating 3d static object lod when using tree replacer mods like realistic aspen trees, etc. 

Docs/trees.ultra/DynDOLOD-Trees.html

Docs/trees.ultra/tools/DynDOLOD_CreateStaticTree.html

 

I have quite a few questions, but we can start with this. In the base resources for sse dyndolod, there is included several treeaspenXpassthru_lod.nif that i assume will be used when you generate 3d SO lod for these trees. But, realistic aspen trees mod is just a replacer, so how will dyndolod know it should use treeaspenX_XXXXXXXXpassthru_lod.nif in \Meshes\DynDOLOD\lod\trees\rat\ instead of default ones?

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You want to use the second rule, so that the higher LOD levels use the billboards. The first rule can end up using the 3D LOD models (or full models even if fallback is set to it) in the higher LOD levels. That typically will demand too much from the engine.

To better understand the 3 different UV conversion scenarios I talked about, it helps to run LODGen for a single tree for example and then check the created BTO for size and in nifskope.
 
To do that, edit DynDOLOD\Edit Scripts\Export\LODGen_SSE_Tamriel.txt in notepad. You can see a "header" part where certain settings are defined and the the "body" with a line for each object or tree that look like
 

00000E07	00000000	71609.585937	64077.003906	2981.428222	11.4592	0.0000	63.0254	1.0	RockL01Snow	00010800	Snow	meshes\landscape\rocks\rockl01.nif	meshes\lod\rocks\rockl01_lod_0.nif		 

Just remove all of those lines but the ones you want to be testing. E.g. keep a line that has treepineforestsnow05_026D7A95passthru_lod.nif in it.

Now set Export=1 in in DynDOLOD\Edit Scripts\DynDOLOD\DynDOLOD_SSE.ini and after starting DynDOLOD, you will see two buttons at them bottom "Execute LODGen" and "Rebuide Atlas". They becomes available after changing the world selection to Tamriel.

"Execute LODGen" will use the (edited) LODGen_SSE_Tamriel.txt. Compare size and texture uses of the created BTOs with the new LODGen.exe/LODGenx64.exe I uploaded. Then edit treepineforestsnow05_026D7A95passthru_lod.nif in nifskope, find the [4]BSTriShape with the Name treepineforestsnow01 and change it to treepineforestsnow01 NoReUV. Now Execute LODGen again and compare BTO size and its used textures, it should be smaller, but use the texture atlas.

 

Third option would be to leave the Name in the nif as is (without NoReUV) and install the TexGen rule file I uploaded to Data/DynDOLOD/*.txt. Run TexGen and install its output. Then use the button "Rebuild Atlas", then "Execute LODGen". Again check the created BTOs size and used textures.

 

When generating LOD for a worldspace, the goal is to use a much textures on the atlas as possible, while keeping the file size small. If a shape uses its own single texture then it is preferable that the texture is used by many models combined into one large single shape in a BTO for best performance.

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