Opened 6 months ago

Closed 6 months ago

#17359 closed defect (fixed)

volume onesmask: 'NoneType' object has no attribute 'size'

Reported by: mai.nguyen@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.8.0-57-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /y/people/mrn533/EMAN2_maps/threed_09.hdf

Opened threed_09.hdf as #1, grid size 256,256,256, pixel 2.11, shown at level
3.54e+03, step 1, values uint16  

> open /y/people/mrn533/EMAN2_maps/Grid06_spt_00_threed_07_emptyhead.hdf

Opened Grid06_spt_00_threed_07_emptyhead.hdf as #2, grid size 128,128,128,
pixel 4.22, shown at level 3.64e+03, step 1, values uint16  

> view orient

> volume #1 level 2016

> volume #2 level 2079

> close #2

> open /y/people/mrn533/EMAN2_maps/Grid05_sptcls_03_threed_16_00(emptyhead-
> portal).hdf

Opened Grid05_sptcls_03_threed_16_00(emptyhead-portal).hdf as #2, grid size
128,128,128, pixel 4.22, shown at level 3.78, step 1, values float32  

> volume #2 level 0.8723

> view orient

> close #1

> close #2

> open /y/people/mrn533/EMAN2_maps/EBIC_fullhead_spt00_threed_09.hdf

Opened EBIC_fullhead_spt00_threed_09.hdf as #1, grid size 256,256,256, pixel
2.18, shown at level 3.31e+03, step 1, values uint16  

> volume #1 level 2200

> volume #1 level 2171

> volume #1 style image colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 127,127,127 imageMode orthoplanes

> volume #1 level 1856,0 level 3310,0.8 level 4095,1

> volume #1 level 1856,0 level 2553,0.8281 level 4095,1

> volume #1 level 1893,0.1719 level 2553,0.8281 level 4095,1

> volume #1 level 1893,0.1719 level 2553,0.8281 level 3852,0.4219

> open /y/people/mrn533/EMAN2_maps/CcGTA_expandedhead_spt00_threed_11.hdf

Opened CcGTA_expandedhead_spt00_threed_11.hdf as #2, grid size 256,256,256,
pixel 2.11, shown at level 3.56e+03, step 1, values uint16  

> volume #2 level 2389

> open /y/people/mrn533/EMAN2_maps/EBIC_fullhead_spt01_threed_07.hdf

Opened EBIC_fullhead_spt01_threed_07.hdf as #3, grid size 256,256,256, pixel
2.18, shown at level 3.3e+03, step 1, values uint16  

> volume #3 level 2100

> volume #3 level 2078

> volume #3 level 2262

> view orient

[Repeated 1 time(s)]

> volume #3 orthoplanes xyz positionPlanes 128,128,128 style image region all

> mousemode rightMode "move planes"

> ui mousemode right select

> select #3

3 models selected  

> ui mousemode right "mark plane"

> marker #4 position 279,278.6,279.4 color yellow radius 2.18

> volume #2 level 2276

> volume #3 level 1838,0 level 3298,0.8 level 4094,1

> volume #3 level 1838,0 level 2280,0.7688 level 4094,1

> marker #4 position 279,168.2,279.1 color yellow radius 2.18

> ui mousemode right distance

> ui mousemode right select

> select /M:1@M

1 atom, 1 residue, 1 model selected  

> select /M:2@M

1 atom, 1 residue, 1 model selected  

> select #3

3 models selected  

> select #3

3 models selected  

> select add /M:1@M

1 atom, 1 residue, 4 models selected  

> select add /M:2@M

2 atoms, 2 residues, 4 models selected  

> ui mousemode right distance

> ui mousemode right "link markers"

> select add #4/M:1@M

2 atoms, 2 residues, 1 model selected  

> ui mousemode right distance

[Repeated 1 time(s)]

> ui tool show "Marker Placement"

Drag select of 2 atoms  

> ui mousemode right distance

> select subtract #4/M:2@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right distance

Drag select of 2 atoms  
[Repeated 1 time(s)]

> select add #4/M:2@M

2 atoms, 2 residues, 1 model selected  

> ui mousemode right "tape measure"

> ui mousemode right distance

> ui tool show Distances

> distance #4/M:1@M #4/M:2@M

Distance between markers #4/M mark 1 M and mark 2 M: 110.379Å  

> shape sphere center 279.3, 279.3, 279.3 radius 110 color blue mesh true

> select up

2 atoms, 1 pseudobond, 2 residues, 9 models selected  

> select up

2 atoms, 1 pseudobond, 2 residues, 10 models selected  

> select up

2 atoms, 1 pseudobond, 2 residues, 11 models selected  

> shape sphere center 279.3, 279.3, 279.3 radius 111 color blue mesh true

> volume onesmask #4

No surfaces specified  

> volume onesmask #3

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/mask/maskcommand.py", line 75, in ones_mask  
v = ones_volume(surfaces, vpad, spacing, border, value_type = vtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/mask/maskcommand.py", line 98, in ones_volume  
bsize = [s + 2*pad + 2*border for s in bounds.size()]  
^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'size'  
  
AttributeError: 'NoneType' object has no attribute 'size'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/mask/maskcommand.py", line 98, in ones_volume  
bsize = [s + 2*pad + 2*border for s in bounds.size()]  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> volume onemask #3

Expected a density maps specifier or a keyword  

> volume onesmask mask #3

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> volume onesmask #4 onGrid #3

No surfaces specified  

> volume onesmask #3 onGrid #3

Opened EBIC_fullhead_spt01_threed_07.hdf masked as #10, grid size 256,256,256,
pixel 2.18, shown at step 1, values int8  

> volume #10 level 0.7026

> close #10

> volume onesmask #shape onGrid #map

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> volume onesmask #shape onGrid #3

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> volume onesmask #sphere onGrid #3

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> volume onesmask #3

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/mask/maskcommand.py", line 75, in ones_mask  
v = ones_volume(surfaces, vpad, spacing, border, value_type = vtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/mask/maskcommand.py", line 98, in ones_volume  
bsize = [s + 2*pad + 2*border for s in bounds.size()]  
^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'size'  
  
AttributeError: 'NoneType' object has no attribute 'size'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/mask/maskcommand.py", line 98, in ones_volume  
bsize = [s + 2*pad + 2*border for s in bounds.size()]  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 570.124.06
OpenGL renderer: NVIDIA GeForce GT 1030/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: OEGStone
Model: BOAMOT-494
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
Cache Size: 9216 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       7.0Gi       1.9Gi       670Mi       7.5Gi       8.4Gi
	Swap:          4.0Gi          0B       4.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP108 [GeForce GT 1030] [10de:1d01] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GP108 [GeForce GT 1030] [1043:85f4]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (3)

comment:1 by pett, 6 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → volume onesmask: 'NoneType' object has no attribute 'size'

comment:2 by Tom Goddard, 6 months ago

The error from using "volume onesmask #3" is because you need to specify a surface and #3 is instead a volume shown as orthoplanes. Maybe you mistakenly used #3 in the command when you meant #5 which was a sphere surface.

At any rate, ChimeraX should give a clearer error message and I will fix that.

comment:3 by Tom Goddard, 6 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Made the volume onesmask give a clear error message if no surfaces were specified.

Note: See TracTickets for help on using tickets.