Segger: Color array dimension 3 must be one more than index array dimension 1

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-58-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open figure/K2_F3_job940_mag_postprocess_hidedust.mrc

Opened K2_F3_job940_mag_postprocess_hidedust.mrc as #1, grid size 800,800,800,
pixel 2.2, shown at step 1, values float32  

> open
> /beebylab/home/tina/projects/fitting/blowout/K2_F3_job940_mag_postprocess.seg

Summary of feedback from opening
/beebylab/home/tina/projects/fitting/blowout/K2_F3_job940_mag_postprocess.seg  
---  
notes | Volume data not found  
Showing 19 region surfaces  
  
Opened K2_F3_job940_mag_postprocess.seg  
Showing K2_F3_job940_mag_postprocess.seg - 19 regions, 19 surfaces  

> set bgColor white

> volume level 0.00125 step 1 region all style surface

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> ui tool show "Color Zone"

> ui tool show "Surface Zone"

> ui tool show "Segment Map"

> volume #1 change image level -0.0006762,0 level 0.006742,0.8 level 0.01525,1

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select clear

> select add #2.7

1 model selected  

> color #2.7 #95661b transparency 0

[Repeated 1 time(s)]

> select subtract #2.7

Nothing selected  

> select add #2.1

1 model selected  

> color #2.1 #9a75ff transparency 0

[Repeated 1 time(s)]

> select subtract #2.1

Nothing selected  

> select add #2.2

1 model selected  

> color #2.2 #d3d7cf transparency 0

[Repeated 1 time(s)]

> select subtract #2.2

Nothing selected  

> select add #2.3

1 model selected  

> hide #2.3 models

> show #2.3 models

> color #2.3 #d3d7cf transparency 0

[Repeated 1 time(s)]

> select subtract #2.3

Nothing selected  

> select add #2.4

1 model selected  

> color #2.4 #94e47d transparency 0

[Repeated 1 time(s)]

> select subtract #2.4

Nothing selected  

> select add #2

20 models selected  

> select subtract #2

Nothing selected  

> select add #2.5

2 models selected  

> select clear

> select subtract #2.5

Nothing selected  

> select add #2.5

1 model selected  

> select subtract #2.5

Nothing selected  

> select add #2.6

1 model selected  

> select add #2.18

2 models selected  

> select subtract #2.6

1 model selected  

> select subtract #2.18

Nothing selected  

> hide #2.18 models

> hide #2.16 models

> show #2.16 models

> hide #2.19 models

> show #2.19 models

> hide #2.16 models

> show #2.16 models

> hide #2.16 models

> show #2.16 models

> color #2.16 #40bfa3 transparency 0

[Repeated 1 time(s)]

> hide #2.16 models

> hide #2.15 models

> show #2.15 models

> hide #2.14 models

> show #2.14 models

> hide #2.13 models

> show #2.13 models

> hide #2.12 models

> show #2.12 models

> hide #2.11 models

> show #2.11 models

> hide #2.10 models

> show #2.10 models

> hide #2.8 models

> show #2.8 models

> hide #2.7 models

> show #2.7 models

> hide #2.7 models

> hide #2.6 models

> show #2.6 models

> color #2.6 #94e47d transparency 0

> hide #2.6 models

> hide #2.4 models

> hide #2.1 models

> hide #2.2 models

> hide #2.3 models

> hide #2.5 models

> show #2.5 models

> color #2.5 #365cf5 transparency 0

[Repeated 1 time(s)]

> hide #2.5 models

> hide #2.8 models

> show #2.8 models

> color #2.8 #ffd479 transparency 0

[Repeated 1 time(s)]

> hide #2.8 models

> hide #2.9 models

> show #2.9 models

> color #2.9 #f3b5dd transparency 0

[Repeated 1 time(s)]

> hide #2.9 models

> hide #2.10 models

> show #2.10 models

> color #2.10 #ee6159 transparency 0

[Repeated 1 time(s)]

> hide #2.10 models

> hide #2.11 models

> show #2.11 models

> color #2.11 #76d6ff transparency 0

[Repeated 1 time(s)]

> hide #2.11 models

> hide #2.12 models

> show #2.12 models

> color #2.12 #94e47d transparency 0

[Repeated 1 time(s)]

> hide #2.12 models

> hide #2.13 models

> show #2.13 models

> color #2.13 #9a75ff transparency 0

[Repeated 1 time(s)]

> hide #2.13 models

> hide #2.14 models

> show #2.14 models

> color #2.14 #9a75ff transparency 0

> hide #2.14 models

> hide #2.15 models

> show #2.15 models

> color #2.15 #ff9800 transparency 0

[Repeated 1 time(s)]

> hide #2.17 models

> show #2.17 models

> hide #2.19 models

> show #2.19 models

> color #2.19 #ff9800 transparency 0

> hide #2.15 models

> hide #2.19 models

> color #2.17 #9a75ff transparency 0

> show #2.1 models

> show #2.2 models

> show #2.3 models

> show #2.5 models

> show #2.4 models

> show #2.6 models

> show #2.7 models

> show #2.8 models

> show #2.9 models

> show #2.10 models

> show #2.11 models

> show #2.12 models

> show #2.13 models

> hide #2.13 models

> show #2.14 models

> hide #2.14 models

> show #2.13 models

> show #2.14 models

> show #2.15 models

> show #2.16 models

> show #2.18 models

Saved  

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #2.18 models

> show #2.18 models

> color #2.18 white transparency 0

> color #2.18 #e21c1c transparency 0

> color #2.18 #e21c1c00

[Repeated 1 time(s)]

> show #2.19 models

> hide #2.19 models

> show #2.19 models

> hide #!2 models

> save /beebylab/home/tina/projects/fitting/whole-motor-map.cxs includeMaps
> true

> view orient

> camera ortho

> turn x -90

> windowsize 1200 1200

[Repeated 1 time(s)]

> lighting soft

> clip

> view orient

> ~clip

> turn x -90

> turn y 90

> clip

> segmentation colors #2 map #1

No segmentations specified  

> ui tool show "Segment Map"

> surface cap false

[Repeated 1 time(s)]

> surface cap true

[Repeated 1 time(s)]

> surface cap false

[Repeated 1 time(s)]

> surface cap true

[Repeated 1 time(s)]

> surface cap false

[Repeated 1 time(s)]

> ~clip

> clip

> surface cap true

[Repeated 1 time(s)]

> surface cap false

[Repeated 1 time(s)]

> ~clip

> windowsize 1200 1200

> view orient

> turn x -90

> windowsize 1200 1200

> view

> ~clip

> clip

> surface cap true

[Repeated 1 time(s)]

> select #1

4 models selected  

> select clear

> color sel #95661B

> undo

> select clear

> hide #!1.2 models

> show #1.2 models

> show #1.1 models

/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py:1905: FutureWarning: Using a non-tuple
sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]`
instead of `arr[seq]`. In the future this will be interpreted as an array
index, `arr[np.array(seq)]`, which will result either in an error or a
different result.  
m = mask[s]  
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.  
  
Color array dimension 3 must be one more than index array dimension 1  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 242, in _draw_scene  
draw_transparent(r, transparent_drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1531, in draw_transparent  
r.draw_transparent(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1242, in draw_transparent  
draw()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1533, in <lambda>  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1539, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 783, in draw  
pd = self._update_planes(renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 551, in _update_planes  
pd = self._update_2d_texture_planes(view_dir)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 559, in _update_2d_texture_planes  
pd = self._texture_2d_planes(axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 585, in _texture_2d_planes  
pd = self._make_planes(axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 713, in _make_planes  
d = Texture2dPlanes(self, axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 984, in __init__  
self._update_textures(planes)  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1063, in _plane_texture  
self._fill_plane_texture(k, axis, t)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1082, in _fill_plane_texture  
data = ir._color_plane(plane, axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 254, in _color_plane  
self.mask_colors(colors, region)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 1909, in cm  
_map.indices_to_colors(ms, cmap, colors, modulate = True)  
TypeError: Color array dimension 3 must be one more than index array dimension
1  
  




OpenGL version: 3.3.0 NVIDIA 460.32.03
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=mate
XDG_SESSION_DESKTOP=mate
XDG_CURRENT_DESKTOP=MATE
DISPLAY=:0
Manufacturer: HP
Model: HP Z1 Entry Tower G5
OS: Linux Mint 20.1 ulyssa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
Cache Size: 16384 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       9.7Gi        46Gi       241Mi       5.9Gi        51Gi
	Swap:          14Gi       3.7Gi        11Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop 9 Series) [8086:3e98] (rev 02)	
	DeviceName: Onboard IGD	
	Subsystem: Hewlett-Packard Company UHD Graphics 630 (Desktop 9 Series) [103c:8591]

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Tom Goddard]

Fixed in 1.5 and daily builds.

Segger menu Regions / Color Density Map never worked in ChimeraX for image style rendering because of changes in how mask colors were computed per plane. I guess no one uses this.