Opened 5 years ago

Closed 5 years ago

#4428 closed defect (fixed)

"mark connected" with no surfaces: ValueError: shapes 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
Used mark connected on a frame with no surface, and returned an error. It should probably just return null and move on. There were other surfaces later in time, just not in the first couple timepoints.

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 Z:\data\Phagocytosis\2019-06-14-YML-sRBC-CF568Mem-Macro-
> NeonGFPMem\CS1-IgGMono-L560nm50p10ms-L488nm30p10ms\Cell_1\Cropped\\*ch0*.tif

Opened map series
Cell_CamB_ch0_stack0000_488nm_0000000msec_0003687647msecAbs_decon.tif as #1,
150 images, grid size 873,768,229, pixel 1, shown at level 322, step 4, values
uint16  

> volume #1.1 step 2

> volume #1.1 level 129.8

> volume #1.1 level 75.85

> open Z:\data\Phagocytosis\2019-06-14-YML-sRBC-CF568Mem-Macro-
> NeonGFPMem\CS1-IgGMono-L560nm50p10ms-L488nm30p10ms\Cell_1\Cropped\\*ch1*.tif

Opened map series
Cell_CamA_ch1_stack0000_560nm_0000000msec_0003687647msecAbs_decon.tif as #2,
150 images, grid size 873,768,229, pixel 1, shown at level 15, step 4, values
uint16  

> close

> open X:\For_Brandon\20190614-sRBC_CS1\\*488nm*.tif

Opened map series
Cell_CamB_ch0_stack0000_488nm_0000000msec_0003687647msecAbs_decon.tif as #1,
150 images, grid size 873,768,229, pixel 1, shown at level 322, step 4, values
uint16  

> volume #1.1 level 104.3

> volume #1.1 step 2

> open X:\For_Brandon\20190614-sRBC_CS1\\*560nm*.tif

Opened map series
Cell_CamA_ch1_stack0000_560nm_0000000msec_0003687647msecAbs_decon.tif as #2,
150 images, grid size 873,768,229, pixel 1, shown at level 15, step 4, values
uint16  

> volume #2.1 step 2

> volume #2.11 level 83.89

> surface dust #1 size 20

> surface dust #2 size 20

> marker connected #2

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.  
  

> marker connected #2

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.  
  

> marker connected #2.8

Found 5 connected surface pieces  

> marker connected #2.5

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.  
  

> marker connected #2.6

Found 2 connected surface pieces  

> marker connected #2.5

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 451.22
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-5039A-I
OS: Microsoft Windows 10 Education (Build 19042)
Memory: 137,115,049,984
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Xeon(R) W-2133 CPU @ 3.60GHz
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: 1.2.1
    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
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    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 pett, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → "mark connected" with no surfaces: ValueError: shapes not aligned

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

The mark connected command did not properly handle the case when the surface was empty.

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