Opened 5 years ago

Closed 4 years ago

#4012 closed defect (can't reproduce)

Error restoring session with embedded maps; text-color issue in bug reporter

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

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
I have a file with 13 TIFF volumes imported, surfaced, and rendered.  I can save the ChimerX session with noMaps and reopen it without issues days later. When I try to reopen a [√]withMaps version, it throws the logged error.
Unrelated (hi everyone!), but on a Mac in OS 10.15+ darkMode, its really hard to read the deep blue colored text I'm typing in the Report a Bud Description: box right now... too dark. A brighter blue world work.

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/grahamj/Desktop/withMaps.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/Applications/3rd Party
Apps/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore  
obj = sm.restore_snapshot(self, data)  
File "/Applications/3rd Party
Apps/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/session.py", line 219, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
File "/Applications/3rd Party
Apps/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/session.py", line 357, in grid_data_from_state  
array = a.reshape(s['size'][::-1])  
ValueError: cannot reshape array of size 1589248 into shape (97,128,256)  
  
opened ChimeraX session  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon R9 M395X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac17,1
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 428.0.0.0.0
      SMC Version (system): 2.34f3

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H15)
      Kernel Version: Darwin 19.6.0
      Time since boot: 21 days 1:03

Graphics/Displays:

    AMD Radeon R9 M395X:

      Chipset Model: AMD Radeon R9 M395X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6920
      Revision ID: 0x0000
      ROM Revision: 113-C905AA-799
      VBIOS Version: 113-C905A0-007
      EFI Driver Version: 01.00.799
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

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
    appnope: 0.1.0
    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: 1.1.1
    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-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-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
    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
File attachment: withMaps.cxs

withMaps.cxs​

Attachments (3)

withMaps.cxs​ (9.6 MB ) - added by grahamj@… 5 years ago.
Added by email2trac
movie14 IntegratedCell_IMSCcol_unCropped-01.jpg​ (831.0 KB ) - added by grahamj@… 5 years ago.
Added by email2trac
movie13_Chimera_1-Maps.cxs.zip​ (7.0 MB ) - added by grahamj@… 5 years ago.
Added by email2trac

Change History (10)

by grahamj@…, 5 years ago

Attachment: withMaps.cxs​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Error restoring session with embedded maps; text-color issue in bug reporter

comment:2 by Tom Goddard, 5 years ago

The problem is that ChimeraX believes the values of your TIF maps is float64 when in fact it is float32 saved in the session file. I never saw a TIFF with 64-bit float pixel values, and I suspect the Python Image Library is screwing this up, reporting the value type as 64-bit float but then handing me pixels that are 32-bit float, probably because it is not capable of handling 64-bit float pixel values.

Could you provide me one of the TIF files so I can see whether they have 64-bit or 32-bit float values and figure out what code is messing this up. The maps in the session are

Matheus Data for Variance Image Nov 2020/data/6 LMNB1_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/1 DOMAIN_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/4 SON_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/5 HIST1H2BJ_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/8 SLC25A17_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/2 FBL_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/12 PXN_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/13TJP1_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/14 MYH10_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/11 ST6GAL1_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/10 TOMM20_SM3B7.tif
Matheus Data for Variance Image Nov 2020/data/9 LAMP1_SM3B7.tif

comment:3 by Tom Goddard, 5 years ago

By the way, the session looks cool when I load it (making the code assume float64 really means float32), like a colorful eye ball!

in reply to:  5 comment:4 by grahamj@…, 5 years ago 

Hi Tom,
   This noMaps version should work. Yes, Dan had the same problem opening the TIFFs at all with AGAVE. ChimeraX opened them fine… even as a noMaps (Tifs linked file as attached)- just seemed to have trouble saving them in a withMaps .cxs file. Should look like attached when opened (sans labels)


[cid:38e31b51-185d-4c6c-91b2-34dfd5ada588@namprd12.prod.outlook.com]

Added by email2trac

movie13_Chimera_1-Maps.cxs.zip​

by grahamj@…, 5 years ago

Attachment: movie14 IntegratedCell_IMSCcol_unCropped-01.jpg​ added

Added by email2trac

by grahamj@…, 5 years ago

Attachment: movie13_Chimera_1-Maps.cxs.zip​ added

Added by email2trac

in reply to:  8 ; comment:5 by goddard@…, 5 years ago 

You didn't give me a TIF file.  I need a TIF file to understand the bug -- it is the TIF file with 64-bit float pixels that is the problem.  The second session you sent me is the same as the first, and that image is what I see (minus the labels) when I open your original session with the code hacked to work around the bug.

I can fix this bug if I have an example TIF file to test with.  But I would suggest you avoid 64-bit float pixels in TIFF -- I imagine lots of software will fail trying to read that and I can't imagine a reason for needing that kind of precision for statistical data.

in reply to:  9 comment:6 by goddard@…, 5 years ago 

I created a 64-bit float tiff file with imagemagick

convert test.png -monitor -depth 64 -define quantum:format=floating-point -compress None test_float64.tif

and it opened in ChimeraX 1.1.1 and daily builds fine, saved and restored from sessions fine.  So there is something special about your tiff files, maybe some type of compression that causes the problem.  Won't be able to debug without getting an example tiff file from you.

comment:7 by Tom Goddard, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

Do not have an example file that can reproduce this bug.

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