Add segmentation surfaces smoothing

[jesse.hansen@…]

The following bug report has been submitted:
Platform:        macOS-12.6-arm64-arm-64bit
ChimeraX Version: 1.5.dev202210102058 (2022-10-10 20:58:47 UTC)
Description
Add smoothing option to "segmentation surfaces" command.  Current surfaces for mask are stair-stepped.

Log:
UCSF ChimeraX version: 1.5.dev202210102058 (2022-10-10)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> volume new size 100 valueType int32

Opened new as #1, grid size 100,100,100, pixel 1, shown at step 1, values
int32  

> volume erase #1 center 20,20,20 radius 15 value 2

> volume erase #1 center 50,50,50 radius 20 value 1

> view

> segmentation surfaces #1

Created 1 segmentation surfaces, 23584 triangles, subsampled 1  

> hide #!1 models




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 34 days 56 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
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    ChimeraX-CommandLine: 1.2.4
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    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202210102058
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    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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[Tom Goddard]

Begin forwarded message:

From: Jesse HANSEN
Subject: Re: [chimerax-users] segmented tomogram density in chimeraX
Date: October 25, 2022 at 12:29:38 AM PDT
To: Tom Goddard <goddard@sonic.net>
Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>

hi,
thank you, this is a very helpful response!  Using segmentation surface #1 each segment I indeed did get all of the surfaces segmented.  The problem though is that the segmentation was not very smooth so I'd like to now smooth the surfaces in chimeraX.

As a workaround to directly smoothing the surface, I used segmentation color to color the tomogram volume, which seems to have colored as expected.  then I tried "volume splitbyzone #1.2" (for tomogram #1 it has by default #1.1 for surface and #1.2 for image(volume)).  This appears to have executed but I do not get any output sub-volumes separated by color.   

thanks again

Jesse

[Tom Goddard]

Done. Added to ChimeraX 1.5 and daily builds.

I added an option smooth (default false) to the "segmentation surfaces" command that will smooth the surfaces. Also there are two other options that control the degree of smoothing: smoothingIterations (default 10) and smoothingFactor (default 1.0). These are the same parameters used when smoothing is enabled for volume contour surfaces and it uses the same method to do the smoothing, moving every surface vertex a fraction of the way toward the average position of its neighbor vertices.

Example commands

segmentation surfaces #1 smooth true
segmentation surfaces #1 smooth true smoothingIterations 3 smoothingFactor 0.5