Opened 5 months ago
Closed 5 months ago
#17735 closed defect (fixed)
xr is None
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | VR | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.10rc202505160006 (2025-05-16 00:06:03 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.10rc202505160006 (2025-05-16) © 2016-2025 Regents of the University of California. All rights reserved. > open "D:\showcase\Nucleus Segmentation\cancerOrg_Nuc_mito_chimerax.cxs" > format session Opened fullNuc_mito.mrc as #1, grid size 2750,1938,70, pixel 5,5,10, shown at step 1, values float32 Opened nuc_seg_smoothed_scaled_chimerax.mrc as #2, grid size 2120,1412,67, pixel 5,5,10, shown at level 0.844, step 1, values int16 Opened mito_seg_smoothed_scaled_chimerax.mrc as #4, grid size 1097,930,69, pixel 5,5,10, shown at level 5e-05, step 1, values uint8 Log from Thu Jan 30 17:43:34 2025 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 E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/fullNuc_mito.mrc Summary of feedback from opening E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/fullNuc_mito.mrc --- note | E:\Eli\Cancer_organoid\Jan2025\Full_nuc_mito_SEM\fullNuc_mito.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened fullNuc_mito.mrc as #1, grid size 2750,1938,70, pixel 1,1,1, shown at step 1, values float32 > open C:/Users/CryoEM/Downloads/nuc_seg_smoothed_scaled_chimerax.mrc Opened nuc_seg_smoothed_scaled_chimerax.mrc as #2, grid size 2120,1412,67, pixel 5,5,10, shown at level 1, step 4, values int16 > volume #2 level 0.8439 > view orient > volume #1 level 2.268e+04,0 level 3.797e+04,0.8 level 4.574e+04,1 > ui tool show "Map Coordinates" > view orient > volume #2 color #757552 > save > E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/cancerOrg_Nuc_mito_chimerax.cxs > includeMaps true > open E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/mito_seg_amira.mrc Summary of feedback from opening E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/mito_seg_amira.mrc --- note | E:\Eli\Cancer_organoid\Jan2025\Full_nuc_mito_SEM\mito_seg_amira.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened mito_seg_amira.mrc as #3, grid size 2750,1938,70, pixel 1,1,1, shown at step 1, values uint8 > volume #3 region 0,0,0,2749,1937,69 step 4 [Repeated 1 time(s)] > surface #1 smooth factor 0.3 iterations 20 Expected a keyword > surface smooth #1 factor 0.3 iterations 20 No surfaces specified > surface smooth #3 factor 0.3 iterations 20 > surface smooth #3 factor 0.3 iterations 30 > hide #4 models > show #4 models > hide #4 models > hide #5 models > show #5 models > hide #5 models > show #5 models > close #4 > surface smooth #3 factor 0.3 iterations 40 > hide #4 models > hide #5 models > show #5 models > hide #5 models > show #5 models > surface smooth #3 factor 0.4 iterations 40 > hide #5 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #6 models > show #6 models > close #5 > close #4 > volume mask #3 surfaces #6 Opened mito_seg_amira.mrc masked as #4, grid size 1097,930,69, pixel 5,5,10, shown at step 1, values uint8 > volume #3 change image level 0,0 level 0.1,0.8 level 1,1 > close #3 > close #6 > save > E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/mito_seg_smoothed_scaled_chimerax.mrc > models #4 > hide #!4 models > show #!4 models > show #!1 models > show #!2 models > volume #2 step 1 > save > E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/cancerOrg_Nuc_mito_chimerax.cxs > includeMaps true ——— End of log from Thu Jan 30 17:43:34 2025 ——— > view name session-start opened ChimeraX session > xr false > xr true > mousemode setting zoom speed 0.2 started OpenXR rendering SonySRD System, render size 3840 by 2160 > VIEW Unknown command: VIEW > view [Repeated 1 time(s)] > xr true > xr false > mousemode setting zoom speed 1 > xr false Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site- packages\chimerax\cmd_line\tool.py", line 319, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3219, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site- packages\chimerax\vive\xr.py", line 87, in vr stop_vr(session, simplify_graphics) File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site- packages\chimerax\vive\xr.py", line 444, in stop_vr cpos = c.mono_camera_position() ^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site- packages\chimerax\vive\xr.py", line 657, in mono_camera_position xr_fov = xr.field_of_view[eye] ^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'field_of_view' AttributeError: 'NoneType' object has no attribute 'field_of_view' File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site- packages\chimerax\vive\xr.py", line 657, in mono_camera_position xr_fov = xr.field_of_view[eye] ^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 560.94 OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: zh_TW.cp950 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: windows Manufacturer: To Be Filled By O.E.M. Model: W790 WS OS: Microsoft Windows 11 專業版 (Build 26100) Memory: 274,484,432,896 MaxProcessMemory: 137,438,953,344 CPU: 24 Intel(R) Xeon(R) w5-2455X OSLanguage: zh-TW Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.3.0 autocommand: 2.2.2 babel: 2.17.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.3.3 build: 1.2.2.post1 certifi: 2025.4.26 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.3 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.6 ChimeraX-AtomicLibrary: 14.1.18 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10rc202505160006 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 2.5.1 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: 1.6.2 ChimeraX-Label: 1.1.14 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: 2.2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 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: 1.19.1 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: 2.5.2 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: 1.45.1 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: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.10 contourpy: 1.3.2 coverage: 7.8.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 inflect: 7.3.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jaraco.collections: 5.1.0 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.1.0 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 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 platformdirs: 4.2.2 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pywin32: 310 pyzmq: 26.4.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.5 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.13.2 typing_extensions: 4.12.2 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 WMI: 1.5.1 zipp: 3.19.2
Change History (3)
comment:1 by , 5 months ago
Component: | Unassigned → VR |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → xr is None |
comment:2 by , 5 months ago
comment:3 by , 5 months ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
Fixed.
Made "xr off" do nothing if the openxr camera is not the current camera.
Note:
See TracTickets
for help on using tickets.
The user enabled OpenXR then turned it off, then turned it off a second time when it wasn't on. Looks like the code needs some check when OpenXR is turned off when it is not actually enabled but has been turned off before so the OpenXR camera exists. Test a fix on Windows.