Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6008 closed defect (fixed)

Problem opening DICOM data: object of type 'NoneType' has no len()

Reported by: tskillman@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here) Tried to load a DICOM directory. Seemed to start OK but then threw error.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/tskillman/Desktop/Latest Images from Sharey/LITAF-october-
> wt-w1-SA-DAPI-LITAF-NED4-CD63-40x001/C1.nii"
> "C:/Users/tskillman/Desktop/Latest Images from Sharey/LITAF-october-
> wt-w1-SA-DAPI-LITAF-NED4-CD63-40x001/C2.nii"
> "C:/Users/tskillman/Desktop/Latest Images from Sharey/LITAF-october-
> wt-w1-SA-DAPI-LITAF-NED4-CD63-40x001/C3.nii"
> "C:/Users/tskillman/Desktop/Latest Images from Sharey/LITAF-october-
> wt-w1-SA-DAPI-LITAF-NED4-CD63-40x001/C4.nii"

Unrecognized file suffix '.nii'  

> open "C:/Users/tskillman/Desktop/Latest Images from Sharey/LITAF-october-
> wt-w1-SA-DAPI-LITAF-NED4-CD63-40x001.nd2"

Unrecognized file suffix '.nd2'  

> open "D:/BioImage Library/MRI & CT/Liver-Gallbladder-Tumor-DICOM" format
> dicom

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 104, in <lambda>  
lambda *args, ses=session: show_open_folder_dialog(ses), tool_tip="Open folder
data",  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 170, in
show_open_folder_dialog  
_folder_dlg.display(session)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 99, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 168, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\\__init__.py", line 30, in open  
return dicom.open_dicom(session, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom.py", line 24, in open_dicom  
series = find_dicom_series(map_path, log = session.logger, verbose =
kw.get('verbose'))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 32, in find_dicom_series  
series.extend(dicom_file_series(dpaths, log = log, verbose = verbose))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 64, in dicom_file_series  
s.order_slices()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 194, in order_slices  
self._sort_by_z_position(files)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 280, in _sort_by_z_position  
series_files.sort(key = lambda sf: (sf._time, inner_product(sf._position,
z_axis)))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 280, in <lambda>  
series_files.sort(key = lambda sf: (sf._time, inner_product(sf._position,
z_axis)))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\geometry\vector.py", line 55, in inner_product  
if len(u) == 3:  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\geometry\vector.py", line 55, in inner_product  
if len(u) == 3:  
  
See log for complete Python traceback.  
  

> open "D:/BioImage Library/MRI & CT/Liver-Gallbladder-Tumor-DICOM" format
> dicom

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 104, in <lambda>  
lambda *args, ses=session: show_open_folder_dialog(ses), tool_tip="Open folder
data",  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 170, in
show_open_folder_dialog  
_folder_dlg.display(session)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 99, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 168, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\\__init__.py", line 30, in open  
return dicom.open_dicom(session, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom.py", line 24, in open_dicom  
series = find_dicom_series(map_path, log = session.logger, verbose =
kw.get('verbose'))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 32, in find_dicom_series  
series.extend(dicom_file_series(dpaths, log = log, verbose = verbose))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 64, in dicom_file_series  
s.order_slices()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 194, in order_slices  
self._sort_by_z_position(files)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 280, in _sort_by_z_position  
series_files.sort(key = lambda sf: (sf._time, inner_product(sf._position,
z_axis)))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 280, in <lambda>  
series_files.sort(key = lambda sf: (sf._time, inner_product(sf._position,
z_axis)))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\geometry\vector.py", line 55, in inner_product  
if len(u) == 3:  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\geometry\vector.py", line 55, in inner_product  
if len(u) == 3:  
  
See log for complete Python traceback.  
  

> open "D:/BioImage Library/MRI & CT/IMediaExport/DICOM" format dicom

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 104, in <lambda>  
lambda *args, ses=session: show_open_folder_dialog(ses), tool_tip="Open folder
data",  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 170, in
show_open_folder_dialog  
_folder_dlg.display(session)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 99, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 168, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\\__init__.py", line 30, in open  
return dicom.open_dicom(session, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom.py", line 24, in open_dicom  
series = find_dicom_series(map_path, log = session.logger, verbose =
kw.get('verbose'))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 32, in find_dicom_series  
series.extend(dicom_file_series(dpaths, log = log, verbose = verbose))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 64, in dicom_file_series  
s.order_slices()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 194, in order_slices  
self._sort_by_z_position(files)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 280, in _sort_by_z_position  
series_files.sort(key = lambda sf: (sf._time, inner_product(sf._position,
z_axis)))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dicom\dicom_format.py", line 280, in <lambda>  
series_files.sort(key = lambda sf: (sf._time, inner_product(sf._position,
z_axis)))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\geometry\vector.py", line 55, in inner_product  
if len(u) == 3:  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\geometry\vector.py", line 55, in inner_product  
if len(u) == 3:  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 511.23
OpenGL renderer: NVIDIA GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: GL702VSK
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 17,134,493,696
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    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
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
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Change History (5)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem opening DICOM data: object of type 'NoneType' has no len()

comment:2 by Tom Goddard, 4 years ago

The error is because the dicom data file does not supply the ImagePositionPatient header value. The code is attempting to order a stack of 2D images according to their 3D position obtained from this header value. Possibly your dicom stack is not 3D but is instead a 2D time series. I can fix the 2D ordering code to work if it is a time series, although probably this type of DICOM data has never been tried in ChimeraX so more errors are likely.

comment:3 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Code will now sort by TemporalPositionIdentifier instead of ImagePositionPatient when the latter header value is not present. I would expect more errors as this kind of data has apparently not been viewed in ChimeraX. The DICOM spec is several thousand pages and ChimeraX only handles a tiny subset of it.

in reply to:  4 ; comment:4 by tskillman@…, 4 years ago 

Hi ChimeraX team (Tom),

Thanks for looking at this. I just got back from travel and will grab the daily build and test it.

The DICOM dataset I have has a moderate complex folder/file structure. It wasn’t clear to me at what part of this structure I should point to open command.  I did notice that some folders had 1 or 2 non-DICOM images so maybe that caused the problem. I’ll let you know the results of my further testing.

Thanks,
Tom




Thomas L. Skillman
Immersive Science LLC
Seattle WA USA
www.immsci.com
tskillman@immsci.com

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