Volume image opacity is too sensitive where brightness curve is near top of histogram

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.6-x86_64-i386-64bit
ChimeraX Version: 1.6.dev202211082330 (2022-11-08 23:30:49 UTC)
Description

Opacity changes  in image style volume rendering are too sensitive when many planes are shown (e.g. 100) and the transfer function is near 1 (top of histogram).  It goes from rather transparent to fully opaque with just a tiny change of height of the brightness curve on the histogram.

The per-plane opacity is determined as alpha_plane = 1 - (1-alpha_curve)**(1/nplanes).  The nplanes equals the number of displayed planes times the transparency depth parameter (default 0.5).  If nplanes = 100 and alpha_curve = 0.99 then alpha_plane =  0.045.  To get alpha_plane close to 1 requires an absurdly close alpha_curve value to 1, for instance alpha_curve = 1 - 1e-30 gives alpha_plane = 0.5.

The interactive adjustment of the brightness curve height works very poorly to control opacity near height 1.


Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.6.dev202211082330 (2022-11-08)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/data/isonet/neuron/synapse-bin4-5i-demo.rec format
> imodmap

Opened synapse-bin4-5i-demo.rec as #1, grid size 530,831,214, pixel 4, shown
at level 66, step 2, values int8  

> volume #1 style image region 0,0,106,529,830,106 step 1 showOutlineBox true

> volume #1 level 46,0 level 68,0.8 level 115,1

> volume #1 level 46,0 level 65.26,0.9853 level 115,1

> ui mousemode right "crop volume"

> volume #1 region 0,0,106,529,830,132

> volume #1 level 46,0 level 61.76,0.7941 level 115,1

> volume #1 level 46,0 level 63.51,0.1471 level 115,1

> volume #1 level 46,0 level 63.51,0.9853 level 115,1

> volume #1 region 0,0,106,529,830,195

> volume #1 level 46,0 level 61.8,1 level 115,1

> volume #1 level 46,0 level 61.8,0.8971 level 115,1

> volume #1 level 46,0 level 61.12,0.8971 level 115,1

> volume #1 level 46,0 level 61.46,0.8824 level 115,1

> volume #1 transparencydepth 0.1

Expected a keyword  

> help volume

> volume #1 transparency .1

> volume #1 level 46,0 level 63.17,0.6912 level 115,1

> volume #1 level 46,0 level 61.8,0.9265 level 115,1

> volume #1 transparency .5

> volume #1 transparency .1

> volume #1 level 55.89,0 level 61.8,0.9265 level 115,1

> volume #1 level 55.89,0 level 62.83,1 level 115,1

> volume #1 level 54.53,0.02941 level 62.83,1 level 115,1

> volume #1 transparency 1

> volume #1 level 54.53,0.02941 level 64.53,0.9706 level 115,1

> volume #1 level 44.64,0.05882 level 64.53,0.9706 level 115,1




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 451.140.1.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 83 days 23:08

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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[Tom Goddard]

Setting the transparency depth to be a smaller fraction of the total thickness (default is 0.5)

volume #1 transparency 0.1

has the bad effect of making the linear part of the brightness curve ramping from 0 up to 1 much more opaque. Also almost no user is aware of this parameter so having them directly modify it is not feasible.

[Tom Goddard]

I don't have a good idea about how to improve the opacity sensitivity when many planes are shown (> 30). It needs to both handle the high opacity region and also give useful opacity variation in linear ramps from 0 to 1. It will need more study.

If I come up with a better way to interpret the brightness/opacity curve there is the additional issue of how to allow past sessions to still reproduce the old behavior while new sessions give the improved behavior.