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Opened 11 months ago
Closed 10 months ago
#16366 closed defect (fixed)
segmentations mouse mode: list index out of range
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | DICOM | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\Users\Public\sandbox\data\tif\sim\RGBt-grid.512.tif format images
Opened multi-channel map RGBt-grid.512.tif as #1, 24 channels, grid size
512,512,512, pixel 1, shown at step 2, values uint8
> open C:\Users\Public\sandbox\data\tif\sim\RGBt-grid.512.tif format images
Opened multi-channel map RGBt-grid.512.tif as #2, 24 channels, grid size
512,512,512, pixel 1, shown at step 2, values uint8
> hide #!2 models
> close #2
> show #1.9 models
> show #1.17 models
> hide #!1.8 models
> hide #!1.7 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.5 models
> hide #!1.6 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1 models
> show #!1 models
> volume #1.1 level 0,0 level 248,0.8 level 255,1
> volume #1.1 level 0,0 level 255,1 color red color red
> volume #1.9 level 0,0 level 248,0.8 level 255,1
> volume #1.9 level 0,0 level 255,1 color lime color lime
> volume #1.17 level 0,0 level 248,0.8 level 255,1
> volume #1.17 level 0,0 level 255,1 color blue color blue
> volume #1
> volume #1 style mesh
> volume #1 style image
> volume #1 maximumIntensityProjection true
> volume #1 maximumIntensityProjection false
> volume #1 maximumIntensityProjection true
> volume #1 region 0,0,254,511,511,254 step 1 maximumIntensityProjection false
> showOutlineBox true
> volume #1.17 level -0.004175,0 level 255,1
> volume #1 region 0,0,0,511,511,511 step 2
> volume #1 region 0,0,0,511,511,511 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 255,255,255 imageMode orthoplanes
> volume #1.1 orthoplanes xyz positionPlanes 262,255,255
> volume #1.1 orthoplanes xyz positionPlanes 329,255,255
> volume #1.1 orthoplanes xyz positionPlanes 329,255,181
> volume #1 imageMode "box faces"
> volume #1 region 0,0,0,511,511,511 step 2 colorMode auto8 imageMode "tilted
> slab" tiltedSlabAxis -0.5538,0.1256,-0.8231 tiltedSlabOffset -344.6
> tiltedSlabPlaneCount 51
> volume #1 maximumIntensityProjection true imageMode "full region"
> close #1.16
> close #1.15
> close #1.14
> show #1.10 models
> volume #1.10 level 0,0 level 248,0.8 level 255,1
> vr true
started SteamVR rendering
> lighting full
[Repeated 1 time(s)]
> lighting soft
> save C:\Users\scITec/Desktop\image1.png supersample 3
> save C:\Users\scITec/Desktop\image2.png supersample 3
> save C:\Users\scITec/Desktop\image3.png supersample 3
> save C:\Users\scITec/Desktop\image4.png supersample 3
> ui tool show "Side View"
> view orient
> view
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> set bgColor white
> set bgColor gray
> set bgColor black
> volume #!1.1,9,17 showOutlineBox false
> volume #!1.1,9,17 showOutlineBox true
> volume #!1.1,9,17 showOutlineBox false
> volume #1.1 orthoplanes xyz positionPlanes 256,256,256 style image region
> all
> mousemode rightMode "move planes"
> volume #1.9 orthoplanes xyz positionPlanes 256,256,256 style image region
> all
> mousemode rightMode "move planes"
> volume #1.17 orthoplanes xyz positionPlanes 256,256,256 style image region
> all
> mousemode rightMode "move planes"
> volume #1.1 orthoplanes xyz positionPlanes 256,256,256 style image region
> all
> mousemode rightMode "move planes"
> volume #1.9 orthoplanes xyz positionPlanes 256,256,256 style image region
> all
> mousemode rightMode "move planes"
> volume #1.17 orthoplanes xyz positionPlanes 256,256,256 style image region
> all
> mousemode rightMode "move planes"
> volume #!1.1,9,17 region all imageMode "full region"
> volume unzone #!1.1,9,17
> mousemode rightMode "crop volume"
> volume #1.1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 256 tiltedSlabSpacing 1 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.9 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 256 tiltedSlabSpacing 1 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.17 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 256 tiltedSlabSpacing 1 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #!1.1,9,17 region all imageMode "full region"
> volume unzone #!1.1,9,17
> mousemode rightMode "crop volume"
> volume #!1.1,9,17 style surface
> volume #!1.1,9,17 style mesh
> volume #!1.1,9,17 style image
[Repeated 1 time(s)]
> volume #!1.1,9,17 showOutlineBox false
VR mode crop volume
> volume #1.1 region 0,0,0,511,511,511
> segmentations handModes true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1306, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\\__init__.py", line 78, in run_provider
return run_toolbar_button(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\actions\\__init__.py", line 73, in
run_toolbar_button
run(session, "segmentations handModes on")
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\cmd\segmentations.py", line 147, in
segmentations
is_vr = save_hand_bindings(session, settings.vr_handedness)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentation_mouse_mode.py", line 180, in
save_hand_bindings
hc = hclist[0]
~~~~~~^^^
IndexError: list index out of range
IndexError: list index out of range
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentation_mouse_mode.py", line 180, in
save_hand_bindings
hc = hclist[0]
~~~~~~^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 556.12
OpenGL renderer: NVIDIA GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: G7 7700
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 16,929,980,416
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → DICOM |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → segmentations mouse mode: list index out of range |
comment:2 by , 10 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
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This should be fixed in the 1.9 release or the daily builds. Sorry for the inconvenience, but please try installing a newer ChimeraX.