Opened 5 years ago

Closed 5 years ago

#4250 closed defect (nonchimerax)

Scipion/Volume Viewer histogram: cannot convert float NaN to integer

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-133-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 266, in _strptime  
month = _months.index(month_name)  
ValueError: tuple.index(x): x not in tuple  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 342, in initialize  
api._api_caller.initialize(api, session, self)  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1265, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 38, in nag  
_check_usage(session)  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 192, in _check_usage  
usage = _get_usage()  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 228, in _get_usage  
usage["dates"].append(_strptime(value))  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 275, in _strptime  
raise ValueError("time data does not match format")  
ValueError: time data does not match format  
  

> runscript
> /home/estrellafg/ScipionUserData/projects/volsub4/Runs/003901_ChimeraSubtractionMaps/tmp/chimeraScript.cxc

> open
> /home/estrellafg/ScipionUserData/projects/volsub4/Runs/003901_ChimeraSubtractionMaps/tmp/axis_input.bild

Opened BILD data containing 6 objects  

> cofr 0,0,0

> open
> /home/estrellafg/ScipionUserData/projects/volsub4/Runs/003831_ProtImportVolumes/extra/import_normalized_20259_resample.mrc

Opened import_normalized_20259_resample.mrc, grid size 288,288,288, pixel
1.03, shown at level 5.03, step 2, values float32  

> volume #2 style surface voxelSize 1.030000

> volume #2 origin -348.16,-97.92,156.40

> open
> /home/estrellafg/ScipionUserData/projects/volsub4/Runs/003831_ProtImportVolumes/extra/import_normalized_EMD-20259.mrc

Opened import_normalized_EMD-20259.mrc, grid size 288,288,288, pixel 1.03,
shown at level 5.15, step 2, values float32  

> rename #3 id #7

> volume #7 style surface voxelSize 1.030000 step 1

> volume #7 origin -348.16,-97.92,156.40

> volume subtract #2 #7 modelId #8 minRms true onGrid #2

Minimum RMS scale factor for "import_normalized_EMD-20259.mrc #7" above level
5.1459 is nan  
  

> scipionwrite #8 prefix difference_

scipionwrite cannot be called from Analyze or Viewers  

> volume gaussian #8 sDev 1.500 modelId 9

> scipionwrite #9 prefix filtered_

scipionwrite cannot be called from Analyze or Viewers  

> scipionss

Saving session  
scipionwrite cannot be called from Analyze or Viewers  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map_data/arrays.py:152: RuntimeWarning: invalid value
encountered in multiply  
v = fbc + b * bsize # Center of bin where rank crossed.  
Traceback (most recent call last):  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2702, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2724, in update_histogram  
counts = s.bin_counts(bins)  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map_data/arrays.py", line 118, in bin_counts  
b0 = int(ceil(fb0))  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map_data/arrays.py", line 118, in bin_counts  
b0 = int(ceil(fb0))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2702, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2724, in update_histogram  
counts = s.bin_counts(bins)  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map_data/arrays.py", line 118, in bin_counts  
b0 = int(ceil(fb0))  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File "/home/estrellafg/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map_data/arrays.py", line 118, in bin_counts  
b0 = int(ceil(fb0))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: GeForce GTX 1060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Alienware
Model: Alienware 15 R4
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
Cache Size: 9216 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            31G        4.3G         19G        133M        7.1G         26G
	Swap:           31G          0B         31G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP106M [GeForce GTX 1060 Mobile] [10de:1c20] (rev a1)	
	Subsystem: Dell Device [1028:0887]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-ScipionExtensions: 1.2
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Scipion/Volume Viewer histogram: cannot convert float NaN to integer

comment:2 by Tom Goddard, 5 years ago

Resolution: → nonchimerax
Status: assigned → closed

User opened MRC map file with NaN intensity values.

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