segmentation surfaces: no attribute 'find_attribute'

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202006162119 (2020-06-16 21:19:45 UTC)
Description
Segmentation surface command on non-hdf5 file.

Log:
UCSF ChimeraX version: 1.1.dev202006162119 (2020-06-16)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/sfftk-rw/sfftkrw/test_data/sff/v0.8/emd_1014.sff
> format sff

Read segmentation file /Users/goddard/ucsf/sfftk-
rw/sfftkrw/test_data/sff/v0.8/emd_1014.sff  
Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-
related bacteriophage PRD1 and shows key capsid and membrane interactions  

> usage segmentation

segmentation colors segmentations [color] [map a density map specifier]
[surface a surface specifier] [byAttribute a text string] [outsideColor a
color] [maxSegmentId an integer] [step map step]  
— Set segmentation to use random colors, or apply segmentation coloring to a
volume  
color: a color

segmentation surfaces segmentations [where where] [each a text string] [region
map region] [step map step] [color a color]  
— Create surfaces for a segmentation regions.  
where: a text string, repeatable  

> segmentation surfaces #1.2

Segmentation region map (#1.2) has 15578 segments (> 100). To create surface
for each segment use "each segment" option.  

> segmentation surfaces #1.2 each 15570-15578

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 263, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segment/segment.py", line 291, in segmentation_surfaces  
region=region, step=sstep, color=color)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segment/segment.py", line 321, in
calculate_segmentation_surfaces  
group, attribute_name = _which_segments(seg, conditions)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segment/segment.py", line 268, in _which_segments  
av = _attribute_values(segmentation, attribute_name)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segment/segment.py", line 420, in _attribute_values  
g = seg.data.find_attribute(attribute_name)  
AttributeError: 'ArrayGridData' object has no attribute 'find_attribute'  
  
AttributeError: 'ArrayGridData' object has no attribute 'find_attribute'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segment/segment.py", line 420, in _attribute_values  
g = seg.data.find_attribute(attribute_name)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 6 days 23:38

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tom Goddard]

Fixed.

Code was trying to use find_attribute() method that is only available on HDF5 volumes.