vop subtract: ArrayMemoryError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/guiis/Downloads/cryosparc_P4_J663_007_volume_map.mrc

Opened cryosparc_P4_J663_007_volume_map.mrc as #1, grid size 1000,1000,1000,
pixel 1.1, shown at step 1, values float32  

> open C:/Users/guiis/Downloads/cryosparc_P4_J442_008_volume_map.mrc

Opened cryosparc_P4_J442_008_volume_map.mrc as #2, grid size 1000,1000,1000,
pixel 1.1, shown at step 1, values float32  

> volume flip #1

Opened cryosparc_P4_J663_007_volume_map.mrc z flip as #3, grid size
1000,1000,1000, pixel 1.1, shown at step 1, values float32  

> volume #2 region 0,0,0,999,999,999 step 4

[Repeated 1 time(s)]

> volume #3

> close #1

> lighting soft

> volume #2 change image level -0.005826,0 level 0.04374,0.8 level 0.1015,1

> volume #2 level 0.02262

> volume #2 level 0.01549

> volume #2 step 1

Could not allocate 3815 Mbyte array of size 1000,1000,1000 and type float32.  
  

> volume #3 level 0.03577

Could not allocate 3815 Mbyte array of size 1000,1000,1000 and type float32.  
  
[Repeated 8 time(s)]

> volume #2 step 2

> volume #3 step 2

> volume #2 level 0.01581

> volume #2 level 0.01646

> volume #3 level 0.03445

> volume #3 level 0.03524

> ui tool show "Fit in Map"

> volume #2 color #d2ffff

> volume #2 color #bfe8e8

> volume #2 color #9ec8e8

> volume #2 color #a4cff0

> volume #3 color #6378b2

> volume #3 color #b2a05d

> volume #3 color #b2b231

> volume #3 color #f5f543

> volume #3 color #f5edb1

> volume #3 color #fef6b7

> volume #3 color #fee1b3

> volume #3 color #fefcb6

> volume #3 color #fee3ad

> fitmap #2 inMap #3

Fit map cryosparc_P4_J442_008_volume_map.mrc in map
cryosparc_P4_J663_007_volume_map.mrc z flip using 2562832 points  
correlation = 0.8606, correlation about mean = 0.5808, overlap = 3151  
steps = 28, shift = 1.1, angle = 0.000463 degrees  
  
Position of cryosparc_P4_J442_008_volume_map.mrc (#2) relative to
cryosparc_P4_J663_007_volume_map.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00000079 -0.00000112 -0.00609690  
0.00000079 1.00000000 -0.00000797 0.00317515  
0.00000112 0.00000797 1.00000000 -1.10097538  
Axis 0.98543937 -0.13901334 0.09790066  
Axis point 0.00000000 136728.95550903 -1594.57989707  
Rotation angle (degrees) 0.00046342  
Shift along axis -0.11423573  
  

> view orient

[Repeated 1 time(s)]

> turn z 180 models #1

> turn z 90 models #1

> view orient

> volume #3 level 0.03457

> volume #3 level 0.03502

> view orient

[Repeated 1 time(s)]

> turn x 90 models #1 #2

> undo

> turn x 90 models #2 #3

> save C:/Users/guiis/Downloads/overlap.jpg width 652 height 443 supersample 3

> save "C:/Users/guiis/Downloads/overlap supersample none.jpg" width 652
> height 443 supersample 1

> save C:/Users/guiis/Downloads/overlap.png width 652 height 443 supersample 3
> transparentBackground true

> turn y 1 360

[Repeated 2 time(s)]

> view orient

> stop

> view orient

> turn y 1 360 frames 360

Repeated keyword argument "frames"  

> turn y 1 360 frames 360

Repeated keyword argument "frames"  

> turn y 1 360 frames 360

Repeated keyword argument "frames"  

> turn y 360 frames 360

> turn y 1 frames 360

> stop

> view orient

> turn y 360 frames 180

> turn y 360 duration 5

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 360 duration 5

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 360 duration 5

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 360 duration 5

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 360 duration

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 360 duration forever

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 360 forever

[Repeated 1 time(s)]

> turn y 1 360 frames 360

Repeated keyword argument "frames"  

> turn y 360 frames 360

> turn y 360 frames 1

> turn y 1 frames 360

> turn y 1 frames 360 duration 5

Expected a keyword  

> turn y 1 frames 360

> stop

> view orient

> turn y 360 frames 360

> turn y 1 frames 360 stop 360

Expected a keyword  

> turn y 1 frames 360 stop 1

Expected a keyword  

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> save C:/Users/guiis/Downloads/overlap.tif width 652 height 443 supersample 3

No map chosen to save  

> view orient

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> cd C:/Users/guiis/Downloads

Current working directory is: C:\Users\guiis\Downloads  

> save C:\Users\guiis\Downloads\image1.png supersample 3

> view orient

> save C:\Users\guiis\Downloads\image2.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\guiis\Downloads\movie1.mp4

Movie saved to \C:Users\\...\Downloads\movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\guiis\Downloads\movie2.mp4

Movie saved to \C:Users\\...\Downloads\movie2.mp4  
  

> movie record

> turn y 360 duration 4

Expected 'forever' or an integer >= 1 or a keyword  

> movie encode output giro360.mp4 width 1920 height 1080

Expected ',' or a keyword  

> stop

> view orient

> turn y 1 frames 360

> view orient

> stop

> view orient

> movie record

Already recording a movie  

> turn y 1 frames 360 movie encode output giro360.mp4 width 1920 height 1080

Expected a keyword  

> movie record turn y 1 frames 360 movie encode output giro360.mp4 width 1920
> height 1080

Expected a keyword  

> movie record turn y 1 frame 360 movie encode output giro360.mp4 width 1920
> height 1080

Expected a keyword  

> movie record turn y 1 360 movie encode output giro360.mp4 width 1920 height
> 1080

Expected a keyword  

> movie record transparentBackground true fps 60

Expected a keyword  

> movie record transparentBackground true

Movie recording will save image frames with transparent background but none of
the encoded movie formats handle transparency, so only this option is only
useful to get the individual frame images.  
Transparent background is only supported with PNG format images. Use movie
record option "format png".  

> movie record

Already recording a movie  

> turn y 1 frames 360

> stop

> stop record

Expected fewer arguments  

> stop recording

Expected fewer arguments  

> movie encode

Output directory does not exist: C:\Users\guiis/Desktop  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\guiis\Downloads\movie1.mp4

Movie saved to \C:Users\\...\Downloads\movie1.mp4  
  

> help help:user/tools/toolbar.html

> movie record

> turn y 1 360

> wait

> movie encode Downloads.mp4

Movie saved to Downloads.mp4  
  

> view orient

> movie record

> turn y 1 180

> wait

> movie encode Downloads.mp4

Movie saved to Downloads.mp4  
  

> vop subtract #2 #3 minrms True

Opened volume difference as #1, grid size 1000,1000,1000, pixel 1.1, shown at
step 1, values float32  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1394, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 403, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 421, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 340, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 909, in subtract_maps  
run(session, 'vop subtract #%s #%s minrms True' % (map1.id_string,
map2.id_string))  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3242, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3878, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 948, in volume_subtract  
sv = combine_op(volumes, 'subtract', on_grid, bounding_grid, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 406, in combine_op  
cv = [combine_operation(volumes, operation, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 406, in <listcomp>  
cv = [combine_operation(volumes, operation, subregion, step,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map_filter\vopcommand.py", line 465, in combine_operation  
rv.combine_interpolated_values(v, op, subregion = subregion, step = step,  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1524, in combine_interpolated_values  
scale = -minimum_rms_scale(values, m, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 2587, in minimum_rms_scale  
vc = v.copy()  
^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.73 GiB for an
array with shape (1000, 1000, 1000) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.73 GiB for an
array with shape (1000, 1000, 1000) and data type float32  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 2587, in minimum_rms_scale  
vc = v.copy()  
^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: pt_BR.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Acer
Model: Swift SF314-511
OS: Microsoft Windows 11 Home Single Language (Build 26100)
Memory: 8,375,296,000
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: pt-BR

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[Tom Goddard]

User opened multiple 4 GB maps (1000 x 1000 x 1000 float32) and ran out of memory on machine with 8 GB.