The original reported behavior called out that filling individual channels did not apply to LODs when LOD Model Painting = False.
With changes implemented in 4627582, the initial fill will reach LODs; subsequent fills will not.

Original notes from Nori:
Filling vertex color with a mask doesn't fill fillcolor but maskcolor to its LOD models incorrectly

It seems that this is caused just by a typo in MeshPaintHelpers::SetInstanceColorDataForLOD().

void MeshPaintHelpers::SetInstanceColorDataForLOD(UStaticMeshComponent* MeshComponent,.....
				// Initialize vertex buffer from given color
				ComponentLodInfo.OverrideVertexColors = new FColorVertexBuffer;
				ComponentLodInfo.OverrideVertexColors->InitFromSingleColor(MaskColor, RenderData.GetNumVertices());

I guess InitFromSingleColor(MaskColor...) is wrong and it should be InitFromSingleColor(FillColor...).
JFYI, As a test, I shelved a super small CL to fix it on 4.21. (4575538)

Steps to Reproduce
  1. Download VertPaint_Sample 4.22
  2. Open VertPaint_Sample 4.22 in UE4Editor
  3. Within the Modes Panel, click the Paintbrush (enter Paint Mode)
  4. Make the following changes:
    • Set Color View Mode to RGB
    • Beneath Vertex Painting, disable Blue, Green, and Alpha
    • Confirm LOD Model Painting is disabled
    • Set Paint Color to (R=1, G=0, B=0, A=0)
  5. Select Fill with Selected Color (beneath the Colors button at the top of the dialog)
  6. Enable LOD Model Painting
  7. Scrub the LOD value through all three LODs (they should be red)
  8. Disable the Red Channel
  9. Enable the Green Channel
  10. Set Paint Color to (R=0, G=1, B=0, A=0)
  11. Select Fill with Selected Color
  12. Enable LOD Model Painting. Scrub the LOD value through all three LODs

LOD0 is filled with Yellow.
LODs 1 and 2 are filled with Red

Expected Result:
All LODs are filled with the selected colors after Filling with the selected Color

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Affects Versions4.204.214.22
Target Fix4.23
CreatedNov 19, 2018
ResolvedDec 4, 2018
UpdatedFeb 20, 2019