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In Response to Clonkonaut
Some time ago, Matthi pushed a fix to this bug.

In order to fix this and to be able to create new animations in the future, I tried to re-export the clonk meshes. I pushed this to a new branch: https://git.openclonk.org/openclonk.git/shortlog/refs/heads/clonk_re-export

This is what I have installed:
Blender 2.71
The newest version of Randrian's exporter (at least I hope so but it says 0.6.0).
Ogre Command Line Tools, but I guess, only the XML Converter is needed.
Python 3.5 (but I guess that newest version is fine)
ck's mesh converter tool

This is roughly what I did:
Opening \openclonk-resources\models\Livings\clonk\ClonkOpenRevolution.blender
Make the layer of the desired skin visible
Make the layer of the armature visible (don't know if this is necessary)
Export it, the standard procedure with the exporter
Run mesh-converter.py over the .mesh and .skeleton file

+ for the Alchemist and Steampunk skin:
Manually edit the .mesh file in a text editor (Notepad++ or something that doesn't fuck it up) so it does use 'Clonk.skeleton' instead of what it was before (the .skeleton file link being one of the few plain text parts of the .mesh file)

+ for the Farmer skin:
The UV Image is pointing to a location on Ringwaul's pc. So I did edit the texture to point to the correct file (which should be "//..\clonkFarmer\clonkFarmer.png")
Removed the empty material
Object > Apply > Make Duplicates Real (Shift Ctrl A)
Export
Do the same than with Alchemist/Steampunk: edit the .skeleton link.

This post is meant to collect problems with the new exports and attempt to gradually fix those and hopefully make the clonk exporting process more smooth.

Problems that I saw so far:
The eyes are often closed now. Before, the eyes' bones were often tied into the animations (this is probably a good thing, to decouple eyes from other animations).
Some animations have shifted positions (KneelDown but maybe more).
It looks to me as if some bone positions differ (when aiming e.g.).
With the steampunk skin, there are a few arm polygons / vertices wrongly connected.
The farmer skin is still broken because the hair isn't really properly connected to the mesh (probabyl something with those duplicates?) but I don't know how to fix it.

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