Volume Viewer: RuntimeWarning: overflow encountered in log

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202012112210 (2020-12-11 22:10:09 UTC)
Description
Volume viewer histogram gets RuntmeWarning overflow in log.
Seems like a numpy 1.19.4 bug.  This code duplicates the error:

>>> from numpy import array, float32, log
>>> a = array([913872900.0], float32)
>>> log(a)
<stdin>:1: RuntimeWarning: overflow encountered in log
array([20.633202], dtype=float32)



Log:
UCSF ChimeraX version: 1.2.dev202012112210 (2020-12-11)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/goddard/ucsf/data/hubmap/HBM897.BMRQ.526/output/cytometry/tile/ome-
> tiff/cell_seg.cmap format cmap

Summary of feedback from opening
/Users/goddard/ucsf/data/hubmap/HBM897.BMRQ.526/output/cytometry/tile/ome-
tiff/cell_seg.cmap  
---  
note |
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/tables/leaf.py:402: PerformanceWarning: The Leaf
``/Chimera/image1/data_zyx`` is exceeding the maximum recommended rowsize
(104857600 bytes);  
be ready to see PyTables asking for *lots* of memory and possibly slow  
I/O. You may want to reduce the rowsize by trimming the value of  
dimensions that are orthogonal (and preferably close) to the *main*  
dimension of this leave. Alternatively, in case you have specified a  
very small/large chunksize, you may want to increase/decrease it.  
warnings.warn("""\  
  
Opened cell_seg.cmap as #1, grid size 9408,9072,11, pixel 377,377,1, shown at
step 4, values uint16  

> volume #1 region 0,0,0,9407,9071,10 step 4

> volume #1 region 0,0,0,9407,9071,10 step 4

> volume #1 step 1

/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py:2746: RuntimeWarning: overflow
encountered in log  
h.show_data(log(counts + 1))  




OpenGL version: 4.1 ATI-3.10.18
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: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 17:48

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

Locale: ('en_US', 'UTF-8')
PySide2 version: 5.15.2
Qt version: 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.0
    backcall: 0.2.0
    biopython: 1.78
    blockdiag: 2.0.1
    certifi: 2020.11.8
    cftime: 1.3.0
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    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.9.5
    ChimeraX-AtomicLibrary: 1.1
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    ChimeraX-AtomSearchLibrary: 1.0
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    ChimeraX-BasicActions: 1.1
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    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
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    ChimeraX-Bumps: 1.0
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    ChimeraX-CellPack: 1.0
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    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202012112210
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
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    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
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    ChimeraX-LookingGlass: 1.1
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    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
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    ChimeraX-MDcrds: 2.1
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    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
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    ChimeraX-Modeller: 1.0
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    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.3.1
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
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    ChimeraX-PresetMgr: 1.0.1
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    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
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    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
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    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2.1
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-SeqView: 2.2.1
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    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Tempy: 0.6.0
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    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
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    cxservices: 1.0
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[Tom Goddard]

Seems like a numpy bug. Does not warn if counts is type float64 instead of float32.

[Tom Goddard]

File a numpy bug report

​https://github.com/numpy/numpy/issues/18005

[Tom Goddard]

Fixed.

I changed the volume viewer code to use float64 for counts array avoiding this warning.

Noticed the C++ code is computing counts using int32 array. So that will wrap at 2 billion and cause trouble. Not easy to remedy since our C++ array wrapping does not support 64-bit integers. Could use float64 but that will likely be slower counting values for large maps. So I left int32 code as is.

[Tom Goddard]

For the int32 C++ code, computing the bin uses float multiply, subtract and two compares so adding a double increment is unlikely to make any substantial speed difference.

[Tom Goddard]

Some other fixes for the int32 problem would be to take a 64-bit float array but cast it to 64-bit int in C++ and then convert at end to 64-bit float. Ugly.

[Tom Goddard]

Numpy developers have fixed the underlying bug which was a clang compiler optimizer bug that took out a numpy assembly instruction specifically intended to avoid the overflow. Impressive how fast the numpy developers resolved this.

​https://github.com/numpy/numpy/issues/18005