Drawing map: cannot select an axis to squeeze out which has size not equal to one

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.6.6-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/irinas/Library/CloudStorage/GoogleDrive-iserysheva@gmail.com/My
> Drive/IrinaLab/Lab-presentations/for-tomo-
> presentation/03312023-particleInTomo.cxs" format session

Opened aligned-correct-apix-test-11022022-_203__bin4.hdf as #1, grid size
1008,1000,256, pixel 7.04, shown at step 1, values uint8  
Opened ptcls_in_tomo_aligned-correct-apix-test-11022022-_203_01.hdf as #2,
grid size 1008,1000,256, pixel 7.04, shown at level 193, step 1, values uint8  
Opened aligned-correct-apix-test-11022022-_203__bin4_preproc_good-SR_seg.hdf
as #3, grid size 1008,1000,256, pixel 7.04, shown at level 0.373, step 1,
values float32  
Log from Tue Aug 8 15:23:44 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/gfan1/Documents/data/tomo/triads/03312023-particleInTomo.cxs

Opened aligned-correct-apix-test-11022022-_203__bin4.hdf as #1, grid size
1008,1000,256, pixel 7.04, shown at step 1, values uint8  
Opened ptcls_in_tomo_aligned-correct-apix-test-11022022-_203_01.hdf as #2,
grid size 1008,1000,256, pixel 7.04, shown at level 193, step 1, values uint8  
Opened aligned-correct-apix-test-11022022-_203__bin4_preproc_good-SR_seg.hdf
as #3, grid size 1008,1000,256, pixel 7.04, shown at level 0.373, step 1,
values float32  
Log from Tue Aug 8 13:10:02 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/gfan1/Documents/data/tomo/triads/03312023-particleInTomo.cxs

Opened aligned-correct-apix-test-11022022-_203__bin4.hdf as #1, grid size
1008,1000,256, pixel 7.04, shown at step 1, values uint8  
Opened ptcls_in_tomo_aligned-correct-apix-test-11022022-_203_01.hdf as #2,
grid size 1008,1000,256, pixel 7.04, shown at level 193, step 1, values uint8  
Opened aligned-correct-apix-test-11022022-_203__bin4_preproc_good-SR_seg.hdf
as #3, grid size 1008,1000,256, pixel 7.04, shown at level 0.373, step 1,
values float32  
Log from Fri Mar 31 22:29:33 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/gfan1/Documents/data/tomo/triads/aligned-correct-apix-
> test-11022022-_203__bin4.hdf

Opened aligned-correct-apix-test-11022022-_203__bin4.hdf as #1, grid size
1008,1000,256, pixel 7.04, shown at level 204, step 4, values uint8  

> open /Users/gfan1/Documents/data/tomo/triads/ptcls_in_tomo_aligned-correct-
> apix-test-11022022-_203_01.hdf

Opened ptcls_in_tomo_aligned-correct-apix-test-11022022-_203_01.hdf as #2,
grid size 1008,1000,256, pixel 7.04, shown at level 109, step 4, values uint8  

> volume #1 style image region 0,0,124,1007,999,124 step 1 showOutlineBox true

> volume #1 level 130,0 level 209,0.8 level 255,1

> volume #1 level 63.08,0 level 209,0.8 level 255,1

> volume #1 level 63.08,0 level 208.1,0.7706 level 255,1

> volume #2 style image

> volume #2 style surface

> volume #2 step 1

> volume #2 change image level 109,0 level 123.6,0.8 level 255,1

> volume #2 level 122.2

> open /Users/gfan1/Documents/data/tomo/triads/aligned-correct-apix-
> test-11022022-_203__bin4_preproc_good-SR_seg.hdf

Opened aligned-correct-apix-test-11022022-_203__bin4_preproc_good-SR_seg.hdf
as #3, grid size 1008,1000,256, pixel 7.04, shown at level 0.501, step 4,
values float32  

> volume #3 step 2

> hide #!1 models

> volume #3 level 0.3731

> ui tool show "Hide Dust"

> surface dust #3 size 42.24

> surface dust #3 size 39.75

> surface dust #3 size 520.68

> volume #2 level 148

> volume #2 level 174.2

> select #3

2 models selected  

> select clear

> volume #2 level 173.3

> volume #2 color #54b5f0

> set bgColor white

> volume #3 color #dbf3f3

> volume #3 color #aed7ea

> volume #3 color #b7daea

> volume #2 color #9284e2

> volume #3 color #e8d9f1

> volume #2 color #a7cbe8

> volume #2 color #8abae4

> volume #3 color #f2efd3

> volume #3 color #ede9ba

> volume #2 region 0,0,0,1007,999,255

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> volume #2 level 193.3

> save /Users/gfan1/Documents/data/tomo/triads/03312023-particleInTomo.cxs
> includeMaps true

——— End of log from Fri Mar 31 22:29:33 2023 ———

opened ChimeraX session  

> hide #!2 models

> hide #!3 models

> show #!1 models

> volume #1 level 63.08,0 level 177.9,0.8735 level 255,1

> volume #1 level 51.3,0.02941 level 177.9,0.8735 level 255,1

> volume #1 level 0,0.2206 level 177.9,0.8735 level 255,1

> volume #1 level 0,0.2206 level 178.4,0.8147 level 255,1

> volume #1 level 0,0.02941 level 178.4,0.8147 level 255,1

> set bgColor black

> volume #1 level 0,0.02941 level 176,0.6912 level 255,1

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> hide #!1 models

> show #!3 models

> ui mousemode right "map eraser"

> volume erase #3 center 583.98,7068.9,820.07 radius 1171.9

> volume erase #3 center 1682,7635.3,955.11 radius 1171.9

> show #!2 models

Can only have one displayed volume when erasing  

[Repeated 3 time(s)]

> select add #4

1 model selected  

Can only have one displayed volume when erasing  

[Repeated 1 time(s)]

> hide #!2 models

> volume erase #3 center 2500.2,7556.5,901.37 radius 1170.9

> volume erase #3 center 3645.4,7324.9,905.97 radius 1170.9

> volume erase #3 center 4640.3,7693.9,893.2 radius 1170.9

> volume erase #3 center 6636.2,7472,893.25 radius 1170.9

> volume erase #3 center 5531.4,7994.2,1672.2 radius 1170.9

> volume erase #3 center 5577.9,7990.4,48.778 radius 1170.9

> volume erase #3 center 6556.1,-210.43,810.74 radius 1170.9

> volume erase #3 center 5233,-226.75,966.11 radius 1170.9

> volume erase #3 center 4342.3,-459.28,936.72 radius 1170.9

> volume erase #3 center 3580.9,-693.36,873.45 radius 1170.9

> volume erase #3 center 2680.2,-813.88,175.08 radius 1170.9

> volume erase #3 center 2684,-670.81,1256.5 radius 1170.9

> volume erase #3 center 917.56,-370.12,1284.6 radius 1170.9

> volume erase #3 center 945.92,-344.63,483.02 radius 1170.9

> view orient

> save /Users/gfan1/Documents/data/tomo/triads/03312023-particleInTomo.cxs
> includeMaps true

——— End of log from Tue Aug 8 13:10:02 2023 ———

opened ChimeraX session  

> show #!1 models

> show #!2 models

> hide #!3 models

> save /Users/gfan1/Documents/data/tomo/triads/03312023-particleInTomo.cxs
> includeMaps true

——— End of log from Tue Aug 8 15:23:44 2023 ———

opened ChimeraX session  

> hide #!2 models

> volume #1 step 2

> volume #1 step 4

> volume #1 step 8

> volume #1 step 1

> volume #1 step 2

> volume #1 step 1

> volume #1 step 2

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
cannot select an axis to squeeze out which has size not equal to one  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 177, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 254, in _draw_scene  
draw_transparent(r, transparent_drawings)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1547, in draw_transparent  
r.draw_transparent(  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1252, in draw_transparent  
draw()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1549, in <lambda>  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1555, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 783, in draw  
pd = self._update_planes(renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 551, in _update_planes  
pd = self._update_2d_texture_planes(view_dir)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 559, in _update_2d_texture_planes  
pd = self._texture_2d_planes(axis)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 585, in _texture_2d_planes  
pd = self._make_planes(axis)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 713, in _make_planes  
d = Texture2dPlanes(self, axis)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 984, in __init__  
self._update_textures(planes)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1056, in _update_textures  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1056, in <listcomp>  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1063, in _plane_texture  
self._fill_plane_texture(k, axis, t)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1082, in _fill_plane_texture  
data = ir._color_plane(plane, axis)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 234, in _color_plane  
m = self._matrix_plane(plane, axis)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 211, in _matrix_plane  
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.  
File "<__array_function__ internals>", line 180, in squeeze  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/core/fromnumeric.py", line 1545, in squeeze  
return squeeze(axis=axis)  
ValueError: cannot select an axis to squeeze out which has size not equal to
one  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6.6 (21G646)
      Kernel Version: Darwin 21.6.0
      Time since boot: 54 days 18:30

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        C34H89x:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 100.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[pett]

Despite no email address, the reporter provided the name Irina Serysheva

[Tom Goddard]

It appears the hdf reader returned an array for a single plane that did not have the correct dimensions. The axis perpendicular to the plane did not have size 1 in the array. This seems to have happened when "volume #1 step 2" was used. But just a few commands earlier in the log, the same command produced no error.