Opened 19 months ago

Last modified 19 months ago

#15076 assigned defect

ArtiaX: delete_selected_particles: arrays used as indices must be of integer (or boolean) type

Reported by: chimerax-bug-report@… Owned by: Utz Ermel
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> copick start
> /Users/clinton.potter/Downloads/copick_config_clinton_potter.json

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> ui mousemode shift wheel 'move copick planes'

> ks

Opened TS_7_7 - 10.0 as #3, grid size 630,630,184, pixel 10,10,10, shown at
step 4, values float32  
Opened TS_7_7 - 10.0 as #1.1.1, grid size 630,630,184, pixel 10,10,10, shown
at level 8.03e-06, step 4, values float32  

> artiax clip off

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> artiax clip off

Opened virus-like-particle as #1.2.1.1.1, grid size 78,78,78, pixel 6.67,
shown at level 0.566, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> artiax clip off

Opened ribosome as #1.2.2.1.1, grid size 61,63,61, pixel 6.67,6.67,6.67, shown
at level 0.332, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

> artiax view xy

> artiax tomo #1.1.1 slice 0

> artiax tomo #1.1.1 slice 9

> artiax particles #1.2.2 color 0,36,19,40

> ui mousemode right select

> ui mousemode right "mark plane"

[Repeated 4 time(s)]

> ui mousemode right select

> select #1.2.2.2

1 model selected  

> select #1.2.2.2

1 model selected  
Drag select of 1.1.1 TS_7_7 - 10.0 , surfaces, 1 of 31 instances  

> artiax view xy

> artiax tomo #1.1.1 slice 33

Drag select of 1.1.1 TS_7_7 - 10.0 , surfaces  

> artiax particles #1.2.2 color 0,36,19,0

> artiax particles #1.2.2 color 0,36,19,5

> artiax tomo #1.1.1 slice 96

> artiax tomo #1.1.1 slice 132

> artiax tomo #1.1.1 slice 74

> artiax tomo #1.1.1 slice 125

> volume #1.1.1 step 1,1,1

> artiax tomo #1.1.1 slice 141

> artiax tomo #1.1.1 slice 136

Drag select of surfaces, 1 of 30 instances  

> artiax tomo #1.1.1 slice 136

> artiax particles #1.2.2 color 0,36,19,71

Drag select of 1.1.1 TS_7_7 - 10.0 , surfaces  

> artiax particles #1.2.2 color 0,36,19,0

> artiax view xy

> artiax tomo #1.1.1 slice 165

> artiax tomo #1.1.1 slice 118

> artiax tomo #1.1.1 slice 103

> artiax tomo #1.1.1 slice 36

> ui mousemode right "mark plane"

> marker #1.2.2.3 position 2635,1229,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2465,928.9,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2694,1257,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2467,980.9,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2573,1201,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2710,1224,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2649,1232,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2593,1215,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2443,929.9,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2650,1279,355.4 color #005c3100 radius 10.01

> marker #1.2.2.3 position 2653,1243,355.4 color #005c3100 radius 10.01

> ui mousemode right select

[Repeated 2 time(s)]

> ui mousemode right "mark plane"

> ui mousemode right select

[Repeated 1 time(s)]

> artiax view xy

> artiax particles #1.2.2 color 0,36,19,87

> select clear

[Repeated 2 time(s)]

> select #1.1.1

3 models selected  

> artiax view xy

[Repeated 1 time(s)]

> ui mousemode right 'mark plane'

> marker #1.2.2.3 position 2745,1220,355.4 color #005c31de radius 150

> marker #1.2.2.3 position 2735,1218,355.4 color #005c31de radius 150

> marker #1.2.2.3 position 2761,1219,355.4 color #005c31de radius 150

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/clinton.potter/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/copick/__init__.py",
line 31, in run_provider  
run_provider(session, name)  
File "/Users/clinton.potter/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/toolbar/toolbar.py", line 42, in run_provider  
what(session)  
File "/Users/clinton.potter/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 1335, in
delete_selected_particles  
ids = col.child_ids[ma]  
~~~~~~~~~~~~~^^^^  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File "/Users/clinton.potter/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 1335, in
delete_selected_particles  
ids = col.child_ids[ma]  
~~~~~~~~~~~~~^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z15T0005NLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 21 days, 18 hours, 6 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U3423WE:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    aiobotocore: 2.12.3
    aiohttp: 3.9.5
    aioitertools: 0.11.0
    aiosignal: 1.3.1
    alabaster: 0.7.16
    annotated-types: 0.6.0
    appdirs: 1.4.4
    appnope: 0.1.3
    asciitree: 0.3.3
    asttokens: 2.4.1
    attrs: 23.2.0
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    botocore: 1.34.69
    build: 0.10.0
    certifi: 2022.12.7
    cffi: 1.16.0
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.4.7
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-copick: 0.2.5
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OME-Zarr: 0.5.4
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    click: 8.1.7
    cloudpickle: 3.0.0
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    copick: 0.4.0
    cryptography: 42.0.5
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    dask: 2024.4.2
    debugpy: 1.8.0
    decorator: 5.1.1
    distributed: 2024.4.2
    docutils: 0.19
    executing: 2.0.1
    fasteners: 0.19
    filelock: 3.9.0
    fonttools: 4.47.2
    frozenlist: 1.4.1
    fsspec: 2024.3.1
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    hatchling: 1.24.2
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imageio: 2.34.1
    imagesize: 1.4.1
    importlib-metadata: 7.1.0
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jmespath: 1.0.1
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    lazy-loader: 0.4
    line-profiler: 4.0.2
    locket: 1.0.0
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    multidict: 6.0.5
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numcodecs: 0.12.1
    numexpr: 2.8.8
    numpy: 1.25.1
    ome-zarr: 0.8.3
    openvr: 1.23.701
    packaging: 24.0
    pandas: 2.2.2
    ParmEd: 3.4.3
    parso: 0.8.3
    partd: 1.4.1
    pathspec: 0.12.1
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    pluggy: 1.5.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pyarrow: 16.0.0
    pycollada: 0.7.2
    pycparser: 2.22
    pydantic: 2.7.1
    pydantic-core: 2.18.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    pyspnego: 0.10.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    PyYAML: 6.0.1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    s3fs: 2024.3.1
    scikit-image: 0.23.2
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    smbprotocol: 1.13.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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
    starfile: 0.5.6
    superqt: 0.5.0
    tables: 3.8.0
    tblib: 3.0.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    toolz: 0.12.1
    tornado: 6.4
    traitlets: 5.9.0
    trimesh: 4.3.1
    trove-classifiers: 2024.4.10
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    wrapt: 1.16.0
    yarl: 1.9.4
    zarr: 2.17.2
    zict: 3.0.0
    zipp: 3.18.1

Change History (1)

comment:1 by Eric Pettersen, 19 months ago

Component: Unassigned → Third Party
Owner: set to Utz Ermel
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ArtiaX: delete_selected_particles: arrays used as indices must be of integer (or boolean) type
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