Opened 4 years ago

Closed 4 years ago

#5286 closed defect (duplicate)

marker connected command: ValueError: shapes (0,) and (3,3) not aligned

Reported by: brandon.scott@… 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:        Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202102030836 (2021-02-03 08:36:42 UTC)
Description
Loaded in a timeseries (10 points) that had zero objects in timepoint 1, but had objects in the remaining 9 frames. The expected result was the points to be 'nan' in time 1 but instead an error was thrown.

Log:
UCSF ChimeraX version: 1.2.dev202102030836 (2021-02-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0000_642nm_0000000msec_0019553257msecAbs_decon.tif
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0001_642nm_0010080msec_0019563337msecAbs_decon.tif
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0002_642nm_0020160msec_0019573417msecAbs_decon.tif
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0003_642nm_0030240msec_0019583497msecAbs_decon.tif
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0004_642nm_0040320msec_0019593577msecAbs_decon.tif
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0005_642nm_0050400msec_0019603657msecAbs_decon.tif
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0006_642nm_0060480msec_0019613737msecAbs_decon.tif
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0007_642nm_0070560msec_0019623817msecAbs_decon.tif
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0008_642nm_0080640msec_0019633897msecAbs_decon.tif
> X:/Phagocytosis/miapMrbc/03-01-cs2/Cell_CamA_ch1_stack0009_642nm_0090720msec_0019643977msecAbs_decon.tif

Opened map series
Cell_CamA_ch1_stack0000_642nm_0000000msec_0019553257msecAbs_decon.tif as #1,
10 images, grid size 724,768,281, pixel 1, shown at level 10, step 4, values
uint16  

> volume #1.1 step 2

> volume #1.1 level 85

> surface dust #1 size 30

> marker connected #1

Traceback (most recent call last):  
File "C:\Apps\ChimeraX-Daily\ChimeraX 1.2.dev202102030836\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "C:\Apps\ChimeraX-Daily\ChimeraX 1.2.dev202102030836\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Apps\ChimeraX-Daily\ChimeraX 1.2.dev202102030836\bin\lib\site-
packages\chimerax\markers\cmd.py", line 222, in marker_connected  
scene_centers = surface.scene_position * centers  
File "C:\Apps\ChimeraX-Daily\ChimeraX 1.2.dev202102030836\bin\lib\site-
packages\chimerax\geometry\place.py", line 119, in __mul__  
return m34.apply_matrix(self._matrix, p)  
File "C:\Apps\ChimeraX-Daily\ChimeraX 1.2.dev202102030836\bin\lib\site-
packages\chimerax\geometry\matrix.py", line 22, in apply_matrix  
r = matrix_multiply(points, transpose(tf[:, :3]))  
File "<__array_function__ internals>", line 5, in dot  
ValueError: shapes (0,) and (3,3) not aligned: 0 (dim 0) != 3 (dim 0)  
  
ValueError: shapes (0,) and (3,3) not aligned: 0 (dim 0) != 3 (dim 0)  
  
File "<__array_function__ internals>", line 5, in dot  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 462.96
OpenGL renderer: Quadro M4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7048GR-TR
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 549,626,036,224
MaxProcessMemory: 137,438,953,344
CPU: 40 Intel(R) Xeon(R) CPU E5-2698 v4 @ 2.20GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    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: 1.11.1
    ChimeraX-AtomicLibrary: 1.2.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202102030836
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.6
    ChimeraX-uniprot: 2.1
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.2
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.3.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.14
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.2
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0
    WMI: 1.5.1

Change History (2)

comment:1 by Tom Goddard, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → marker connected command: ValueError: shapes (0,) and (3,3) not aligned

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

This ChimeraX error is from using the "marker connected" command when no surface is shown. It was fixed 6 months ago, bug #4428. Update to the current ChimeraX 1.2.5 to fix this problem.

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