traceback restoring session saved after using Segmentations tool

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-12.6.7-arm64-arm-64bit
ChimeraX Version: 1.7.dev202307260053 (2023-07-26 00:53:22 UTC)
Description
DICOM (Segmentations tool)

Although I can now save a session with a segmentation that was created in this tool (#9394), trying to restore that session gives a traceback.  Session file attached

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html; ui dockable false "Help Viewer"

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html; ui dockable false "Help Viewer"

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

> alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-
> channel.html; ui dockable false "Help Viewer"; windowsize 600 800

executed startup.cxc  
UCSF ChimeraX version: 1.7.dev202307260053 (2023-07-26)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/meng/Desktop/4-24533 format dicom

Summary of feedback from opening /Users/meng/Desktop/4-24533  
---  
note | Opened 4 CT (No Description) as #1.1.1, grid size 512,512,236, pixel
0.576,0.576,1.24, shown at step 1, values int16  
  

> close

> open "/Users/meng/dicom/tcia/Head-Neck Cetuximab-
> Demo/0522c0027/01-19-2000-HEAD NECK IMRT-50644/9611-58470" format dicom

Summary of feedback from opening /Users/meng/dicom/tcia/Head-Neck Cetuximab-
Demo/0522c0027/01-19-2000-HEAD NECK IMRT-50644/9611-58470  
---  
note | Opened 9611 CT () as #1.1.1, grid size 512,512,175, pixel
0.977,0.977,2.98, shown at step 1, values float32  
  

> close

> open /Users/meng/Desktop/11-06-2014-1-96508-subset format dicom

Summary of feedback from opening /Users/meng/Desktop/11-06-2014-1-96508-subset  
---  
notes | Opened 4 CT (No Description) as #1.1.1, grid size 512,512,236, pixel
0.576,0.576,1.24, shown at step 1, values int16  
Opened 1000 SEG (QIN CT challenge: alg02 run1segmentation result) as #1.1.2,
grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5, step 2,
values uint8  
Opened 1000 SEG (QIN CT challenge: alg01 run1segmentation result) as #1.1.3,
grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5, step 2,
values uint8  
Opened 1000 SEG (QIN CT challenge: alg03 run1segmentation result) as #1.1.4,
grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5, step 2,
values uint8  
  

> ui tool show Segmentations

> dicom view fourup

Opened segmentation 1 as #5, grid size 512,512,236, pixel 0.576,0.576,1.24,
shown at level 0.0002, step 2, values int16  
Compositor returned null texture  
[Repeated 1 time(s)]

> save segses.cxs

> close

> open /Users/meng/Desktop/segses.cxs format session

Opened 4 CT (No Description) as #1.1.1, grid size 512,512,236, pixel
0.576,0.576,1.24, shown at step 1, values int16  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

Merged incoming unique studies with existing patient with same ID  

Opened 1000 SEG (QIN CT challenge: alg02 run1segmentation result) as #1.1.2,
grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5, step 2,
values uint8  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Merged incoming unique studies with existing patient with same ID  

Opened 1000 SEG (QIN CT challenge: alg01 run1segmentation result) as #1.1.3,
grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5, step 2,
values uint8  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Merged incoming unique studies with existing patient with same ID  

Opened 1000 SEG (QIN CT challenge: alg03 run1segmentation result) as #1.1.4,
grid size 512,512,236, pixel 0.576,0.576,1.24, shown at level 0.5, step 2,
values uint8  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

[Repeated 1 time(s)]Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 734, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/session.py", line 231, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/session.py", line 396, in grid_data_from_state  
array = a.reshape(s['size'][::-1])  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: cannot reshape array of size 30932992 into shape (236,512,512)  
  
opened ChimeraX session  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.5.2, Qt 6.5.2
Qt runtime version: 6.5.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6.7 (21G651)
      Kernel Version: Darwin 21.6.0
      Time since boot: 4:20

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
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    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46.1
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
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    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
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    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: 1.7.dev202307260053
    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
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    ChimeraX-DistMonitor: 1.4
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    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
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    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
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    pydicom: 2.3.0
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File attachment: segses.cxs

segses.cxs​

[Elaine Meng]

Added by email2trac

[Zach Pearson]

DICOM segmentations were being saved with the wrong numpy value type, which broke the session restore logic. A 512x512x212 array of uint8 can't be reshaped to 512x512x212 of int16 (one example of an attempted restore in my testing). I changed the code so that when segmentations are created they get the right value type of uint8.

The neither segmentation tool nor its cursors nor the view layout are saved in sessions. I opened a DICOM file, opened the segmentation tool, clicked on one of the planes, and saved a session. I was then able to restore the session I saved, which reopened the reference volume and the segmentation.

Subsequent session save/restores should work; let me know if you run into any more issues with tomorrow's build or any build after that one.