Opened 4 years ago

Closed 4 years ago

#4898 closed defect (fixed)

Crash opening TIFF stack

Reported by: chimerax-bug-report@… 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-10-10.0.18363
ChimeraX Version: 1.3.dev202107140317 (2021-07-14 03:17:23 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x00002600 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\map\image3d.py", line 1226 in _perp_planes_geometry
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\map\image3d.py", line 1172 in _update_geometry
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\map\image3d.py", line 1154 in update_view_direction
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\map\image3d.py", line 598 in _update_3d_texture_planes
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\map\image3d.py", line 545 in _update_planes
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\map\image3d.py", line 780 in draw
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\map\image3d.py", line 1361 in draw
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\map\image3d.py", line 770 in draw
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\graphics\drawing.py", line 1511 in _draw_multiple
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\graphics\drawing.py", line 1505 in 
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\graphics\opengl.py", line 1240 in draw_transparent
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\graphics\drawing.py", line 1503 in draw_transparent
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\graphics\view.py", line 240 in _draw_scene
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\graphics\view.py", line 165 in draw
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\core\updateloop.py", line 73 in draw_new_frame
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\core\updateloop.py", line 138 in _redraw_timer_callback
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\ChimeraX_main.py", line 880 in init
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\site-packages\ChimeraX_main.py", line 1029 in 
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3.dev202107140317\bin\lib\runpy.py", line 194 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3.dev202107140317 (2021-07-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open M:/WG-projects-C/LID538-ROI7/8nm/ROIS-rotated/h5-for-
> MIB/2021-02-19-physiology-presentation-crop/Model-tifs/Composite.tif

Opened multi-channel map Composite.tif as #1, 7 channels, grid size
291,324,164, pixel 3.15e-07,3.15e-07,1, shown at step 1, values uint8  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3.dev202107140317 (2021-07-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 462.59
OpenGL renderer: GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Enterprise (Build 18363)
Memory: 274,745,065,472
MaxProcessMemory: 137,438,953,344
CPU: 48 AMD Ryzen Threadripper 3960X 24-Core Processor 
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: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.26
    ChimeraX-AtomicLibrary: 3.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    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: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202107140317
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.4
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.6.1
    ChimeraX-PDB: 2.4.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    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: 1.4.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.10.1
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.3.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.5.1
    numexpr: 2.7.3
    numpy: 1.20.3
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    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: 22.1.0
    qtconsole: 5.1.0
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.0.post1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash opening TIFF stack

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Maybe fixed.

Crash was in box_cuts() computing how perpendicular view planes intersect volume box. There was one place in that code where a divide by zero looks possible. I put in code to avoid divide by zero. Don't have a test case.

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