[chimera-dev] stereo3D focal plane

[Greg Couch]

You could also try turning on the Camera's experimental autoFocus 
capability:

     chimera.viewer.camera.autoFocus = True

It tries to maintain the focal plane at the same relative position 
between the hither and yon planes.   I don't recall why it is off, it 
must have interacted badly with some other feature.  But it might work 
for you :-)

     -- Greg

On 04/23/2015 10:57 AM, Tom Goddard wrote:
> Hi Matt,
>
>   I think the “new frame” trigger is the main useful one.  There are 
> others that tell when molecule colors or display styles change, when 
> atoms get deleted, or models are moved.  We don’t have much 
> programming documentation but there is an example of using triggers to 
> see when atoms change colors.
>
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomTrigger.html
>
>    Tom
>
>
>> On Apr 21, 2015, at 1:24 PM, Dougherty, Matthew T <matthewd at bcm.edu 
>> <mailto:matthewd at bcm.edu>> wrote:
>>
>> thanks.
>>
>> from chimera import triggers
>> triggers.addHandler('new frame', set_focal_plane, None)
>>
>> was the part I could not figure out.  Would like to find out more 
>> about this api and other registered triggers, will look at the code. 
>>  Besides 'new frame', are there any other imporant ones that could 
>> make useful for interfaces?
>>
>> In my user control pane extension I have a focal widget that varies 
>> between -1,0 thru 100.
>> -1 disables the widget. 0-100 is the percentage between near & far 
>> CP. Usually if I am between the two, people's eyes don't bleed, 
>> buying me some time to adjust the percentage correctly.
>>
>>
>>
>> As for zooming, I tell people here not to use it, stick with 
>> z-translation because it gives you a better spatial feel of the data 
>> set, XYZ are in unity.  Plus zooming maxes out and people can't 
>> figure out why, they think they are dollying but are not.  Unless 
>> they can write a command for z translation, they are stuck.
>>
>>
>> Matthew Dougherty
>> National Center for Macromolecular Imaging
>> Baylor College of Medicine
>> ===========================================================================
>> ------------------------------------------------------------------------
>> *From:*Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
>> *Sent:*Tuesday, April 21, 2015 2:57 PM
>> *To:*Dougherty, Matthew T
>> *Cc:*chimera-dev at cgl.ucsf.edu <mailto:chimera-dev at cgl.ucsf.edu>
>> *Subject:*Re: [chimera-dev] stereo3D focal plane
>> Hi Matt,
>>
>>   Here’s some Python that will update the focal plane position to 
>> always lie midway between near and far clip planes.
>>
>>   If you zoom by moving a map or molecule closer to you (z 
>> translation) then visually the map should move from behind the screen 
>> to be in front of the screen so it looks like it is coming closer.   
>> In other words the map moves forward and the focal plane that defines 
>> the position of the screen stays fixed.  That is normal Chimera 
>> behavior.  The above script will defeat that.  You will move the map 
>> closer to you in z, but what you will see in stereo is that the map 
>> gets bigger, but no closer.  It instead feels like a magical scaling 
>> of the map, rather than getting closer to it.  This isn’t natural, 
>> but I understand that because of the limited 3d depth with stereo 
>> viewing it is necessary to do something to avoid uncomfortable stereo 
>> where the models are too far in front of the screen.  An optimal 
>> solution is more subtle than the above script.  In fact the above 
>> script won’t prevent getting the front surface of the map too close 
>> for stereo viewing because it keeps the focal plane at the map 
>> midpoint in z.  The front of the map can still get close to your eye 
>> and the stereo will not work.  Basically you want to avoid having the 
>> front visible part of the models from getting too close to your eye 
>> where the stereo glasses don’t work (because the display screen is 
>> not wide enough).  We have not worked on techniques to avoid stereo 
>> interactive viewing limitations.  But the normal Chimera zoom uses 
>> scale factor, not z-translation, so that is the main way this problem 
>> is avoided.  But you are using z-translation instead of the normal 
>> Chimera zooming and that is why you encounter this problem.
>>
>> Tom
>
>
>
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