'<' not supported between instances of 'IS' and 'NoneType'

[justin.kirby@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6rc202304272016 (2023-04-27 20:16:52 UTC)
Description
I was attempting to load data from TCIA collection CT Lymph Nodes, patient ID = ABD_LYMPH_019.  I think it might have failed in trying to load the SEG series with the CT.  Do you support DICOM SEG?

Log:
UCSF ChimeraX version: 1.6rc202304272016 (2023-04-27)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Download DICOM"

> open 61.7.259229997858724420813408711235467205350 fromDatabase tcia format
> dicom

Summary of feedback from opening 61.7.259229997858724420813408711235467205350
fetched from tcia  
---  
warning | Plane z spacings are unequal, min = -603, max = 619, using max.  
Perpendicular axis (0.000, 0.000, 1.000)  
Directory
C:\Users\kirbyju\Downloads\ChimeraX\tciaDownload\61.7.259229997858724420813408711235467205350  
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1-418.dcm (-176.0, -52.0, -339.6)  
1-171.dcm (-176.0, -52.0, -586.6)  
1-422.dcm (-176.0, -52.0, -335.6)  
1-259.dcm (-176.0, -52.0, -498.6)  
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1-111.dcm (-176.0, -52.0, -646.6)  
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1-221.dcm (-176.0, -52.0, -536.6)  
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1-188.dcm (-176.0, -52.0, -569.6)  
1-635.dcm (-176.0, -52.0, -122.6)  
1-247.dcm (-176.0, -52.0, -510.6)  
1-338.dcm (-176.0, -52.0, -419.6)  
1-232.dcm (-176.0, -52.0, -525.6)  
1-402.dcm (-176.0, -52.0, -355.6)  
1-026.dcm (-176.0, -52.0, -731.6)  
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1-417.dcm (-176.0, -52.0, -340.6)  
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1-361.dcm (-176.0, -52.0, -396.6)  
1-359.dcm (-176.0, -52.0, -398.6)  
1-494.dcm (-176.0, -52.0, -263.6)  
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1-335.dcm (-176.0, -52.0, -422.6)  
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1-227.dcm (-176.0, -52.0, -530.6)  
1-443.dcm (-176.0, -52.0, -314.6)  
1-519.dcm (-176.0, -52.0, -238.6)  
1-243.dcm (-176.0, -52.0, -514.6)  
1-088.dcm (-176.0, -52.0, -669.6)  
1-500.dcm (-176.0, -52.0, -257.6)  
1-049.dcm (-176.0, -52.0, -708.6)  
1-473.dcm (-176.0, -52.0, -284.6)  
1-376.dcm (-176.0, -52.0, -381.6)  
1-558.dcm (-176.0, -52.0, -199.6)  
1-044.dcm (-176.0, -52.0, -713.6)  
1-197.dcm (-176.0, -52.0, -560.6)  
1-125.dcm (-176.0, -52.0, -632.6)  
1-498.dcm (-176.0, -52.0, -259.6)  
1-346.dcm (-176.0, -52.0, -411.6)  
1-236.dcm (-176.0, -52.0, -521.6)  
1-364.dcm (-176.0, -52.0, -393.6)  
1-129.dcm (-176.0, -52.0, -628.6)  
1-150.dcm (-176.0, -52.0, -607.6)  
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1-322.dcm (-176.0, -52.0, -435.6)  
1-071.dcm (-176.0, -52.0, -686.6)  
1-299.dcm (-176.0, -52.0, -458.6)  
1-365.dcm (-176.0, -52.0, -392.6)  
1-380.dcm (-176.0, -52.0, -377.6)  
1-439.dcm (-176.0, -52.0, -318.6)  
1-191.dcm (-176.0, -52.0, -566.6)  
1-103.dcm (-176.0, -52.0, -654.6)  
1-564.dcm (-176.0, -52.0, -193.6)  
1-459.dcm (-176.0, -52.0, -298.6)  
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1-124.dcm (-176.0, -52.0, -633.6)  
1-506.dcm (-176.0, -52.0, -251.6)  
1-399.dcm (-176.0, -52.0, -358.6)  
1-568.dcm (-176.0, -52.0, -189.6)  
1-453.dcm (-176.0, -52.0, -304.6)  
1-167.dcm (-176.0, -52.0, -590.6)  
1-547.dcm (-176.0, -52.0, -210.6)  
1-551.dcm (-176.0, -52.0, -206.6)  
1-217.dcm (-176.0, -52.0, -540.6)  
1-514.dcm (-176.0, -52.0, -243.6)  
1-405.dcm (-176.0, -52.0, -352.6)  
1-094.dcm (-176.0, -52.0, -663.6)  
1-598.dcm (-176.0, -52.0, -159.6)  
1-046.dcm (-176.0, -52.0, -711.6)  
1-141.dcm (-176.0, -52.0, -616.6)  
1-031.dcm (-176.0, -52.0, -726.6)  
1-033.dcm (-176.0, -52.0, -724.6)  
1-384.dcm (-176.0, -52.0, -373.6)  
1-528.dcm (-176.0, -52.0, -229.6)  
1-371.dcm (-176.0, -52.0, -386.6)  
1-387.dcm (-176.0, -52.0, -370.6)  
1-389.dcm (-176.0, -52.0, -368.6)  
1-609.dcm (-176.0, -52.0, -148.6)  
1-058.dcm (-176.0, -52.0, -699.6)  
1-072.dcm (-176.0, -52.0, -685.6)  
1-219.dcm (-176.0, -52.0, -538.6)  
1-411.dcm (-176.0, -52.0, -346.6)  
1-476.dcm (-176.0, -52.0, -281.6)  
1-355.dcm (-176.0, -52.0, -402.6)  
1-492.dcm (-176.0, -52.0, -265.6)  
1-308.dcm (-176.0, -52.0, -449.6)  
note | Opened None CT (abdominal_lymph_nodes) as #1.1.1, grid size
512,512,636, pixel 0.684,0.684,1, shown at step 1, values int16  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.21367.1674506077.389696 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.21367.1674506077.389696 fetched from tcia  
---  
warnings | Plane z spacings are unequal, min = -33, max = 45, using max.  
Perpendicular axis (0.000, 0.000, 1.000)  
Directory
C:\Users\kirbyju\Downloads\ChimeraX\tciaDownload\1.2.276.0.7230010.3.1.3.0.21367.1674506077.389696  
1-1.dcm (-176.0, -52.0, -666.599976)  
Merged incoming unique studies with existing patient with same ID  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\dicom\dicom\ui\dicom_databases.py", line 219, in <lambda>  
self.open_button.clicked.connect(lambda: self._on_open_button_clicked())  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\dicom\dicom\ui\dicom_databases.py", line 337, in
_on_open_button_clicked  
self._on_series_table_double_clicked(self.series_entries.selected)  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\dicom\dicom\ui\dicom_databases.py", line 341, in
_on_series_table_double_clicked  
run(self.session, f"open {item.seriesUid} fromDatabase tcia format dicom")  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\dicom\dicom\dicom_fetcher.py", line 6, in fetch  
return TCIADatabase.getImages(session, ident, ignore_cache)  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\dicom\dicom\databases\tcia.py", line 117, in getImages  
models, msg = DICOM.from_paths(session, final_download_dir).open()  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\dicom\dicom\dicom.py", line 48, in open  
patient.render()  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\dicom\dicom\dicom_hierarchy.py", line 124, in render  
study.series.sort(key = lambda x: x.number)  
TypeError: '<' not supported between instances of 'IS' and 'NoneType'  
  
TypeError: '  
File "C:\Program Files\ChimeraX-04-30-23\bin\lib\site-
packages\chimerax\dicom\dicom\dicom_hierarchy.py", line 124, in render  
study.series.sort(key = lambda x: x.number)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9749
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 7420
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,888,762,368
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    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: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.4
    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: 1.6rc202304272016
    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
    comtypes: 1.1.14
    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: 2022.9.26
    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: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    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
    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
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    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
    pywin32: 305
    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
    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
    WMI: 1.5.1
    zipp: 3.15.0
File attachment: chimerax-error.png

chimerax-error.png​

[justin.kirby@…]

Added by email2trac

[pett]

Reported by Justin Kirby

[Zach Pearson]

This dataset works in the 1.7 daily build. I refactored the DICOM module to accommodate datasets on TCIA that have differently-sized and oriented images in the same series (e.g. some PET scans), and thought it was a little bit risky to backport to 1.6 this close to a release. Can you retry the 1.7 daily build?

[Zach Pearson]

OK, this is a real bug that needed to be patched on both branches. I try to sort series by their number so that they show up nicely in the model panel, and I get the number from files with file.get("number", default). This will actually return None if the number happens to be None, but I've treated that syntax as if it means "1-if-not-x.attr" in a couple places. Will be patched tomorrow.