[Chimera-users] Silhouettes and depth cueing

[Michael Elbaum]

Yes, I'm more interested in the solid colors, which would be rendered by depth. I'm curious if the relative impression of depth would be preserved even if the view direction deviates (perhaps not too much) from the dataset z axis. I'm sure it will be very useful for tomography.
best,
Michael

________________________________
From: Tom Goddard [goddard at sonic.net]
Sent: Tuesday, November 03, 2015 00:27
To: Michael Elbaum
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Silhouettes and depth cueing

Hi Michael,

  It sounds like you want to color solid style volume rendering from the  near z plane to the far z plane of the data set.  The “surface color” tool can make such a gradient, but only on surfaces.  Since the data set z axis is not necessarily aligned with the viewing direction, I don’t call that depth cueing (although I know you use it to indicate depth).  We hope to have more capabilities to color solid style volumes in Chimera 2.

Tom


On Nov 2, 2015, at 1:19 PM, Michael Elbaum wrote:

Hi.

I would like to add to this request. I've used the depth cueing very effectively with 3D chroma glasses that map front-back by red-blue color. Elaine helped me on this a few months ago (May 17-18) and I made a nice rocking movie. The color depth cue works well over the whole volume defined by global clipping planes, but not on a slab defined by the volume viewer planes. That's my feature request for Chimera 2: to allow definition of the color gradient with respect to the visible planes of a volume.

thanks,
Michael


________________________________
From: chimera-users-bounces at cgl.ucsf.edu<mailto:chimera-users-bounces at cgl.ucsf.edu> [chimera-users-bounces at cgl.ucsf.edu<mailto:chimera-users-bounces at cgl.ucsf.edu>] on behalf of Tom Goddard
Sent: Monday, November 02, 2015 22:42
To: Oliver Clarke
Cc: chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> BB
Subject: Re: [Chimera-users] Silhouettes and depth cueing

Hi Oliver,

  In Chimera 2 we can try to have silhouette edges fade with depth.  I’ve attached an example from Chimera 2 where the edges fade and where they don’t fade.  Chimera 1 uses a stencil buffer approach to drawing the edges with old-style OpenGL graphics without shader programs and the depth information is lost.  It would be harder to do in Chimera 1.  I’ve submitted a feature request for Chimera 2 to fade the edges.

Tom

<se_depth.png><se_nodepth.png>


On Nov 2, 2015, at 8:21 AM, Oliver Clarke wrote:

Hi all,

I’ve noticed that the intensity/color of silhouettes does not vary with depth cueing the way everything else does - normally this is fine, except when one is showing a slab of a structure - fragments of secondary structural elements which would otherwise blend into the background tend to become overly emphasized by the presence of silhouettes. The obvious solution to this for now is to turn off silhouettes when making these kinds of figures, but I quite like the effect that silhouettes provide, so I would rather not do so if there is an alternative. Perhaps in Chimera 2 it may be worth considering applying a depth dependent factor to the silhouette color (so it fades into the background color as it approaches the yon clipping plane)?

Cheers,
Oliver.
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