[Chimera-users] save volume histogram transfer function
goddard at cgl.ucsf.edu
Thu Feb 14 10:39:54 PST 2008
Unfortunately the Chimera volume dialog won't tell you the exact
height of the nodes on the histogram. I'll add that to the requested
features list. Attached is a script that will print those values for
the active volume in a format that can be used on other volumes with the
File/Open tfunc.py, reply log shows:
level -6.92021e-16,0 level 0.391341,0.99 level 0.581401,1
Command to use these levels on volume with id 3:
volume #3 level -6.92021e-16,0 level 0.391341,0.99 level 0.581401,1
or on volumes 4 through 8:
volume #4-8 level -6.92021e-16,0 level 0.391341,0.99 level
The pairs of numbers are data value and "brightness" (= height on
histogram, range 0-1). The numbers also appear in Chimera session files
-- search for "solid_levels" to find them. Lastly, the heights of the
intial 3 nodes are always 0, 0.99, and 1.0.
> is there a way for me to save the histogram transfer function that is
> displayed in Volume Viewer? I see that I can write down where the nodes
> are placed as these values appear in the "Level" dialog, but do not see
> a place to input magnitude (or write it down) of each node on the line.
> Ideally, I would just like to save it out, to apply the identical
> transform to multiple segmented areas of a volume.
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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