Opened 6 years ago

Closed 6 years ago

#2293 closed defect (fixed)

cannot save session with volume eraser sphere?

Reported by: Elaine Meng 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:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-08-01)
Description
cannot save session with volume eraser sphere?



Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  

> open startup.cxc

> alias reset view orient; view initial

> alias vmc view selAtoms|selMaps; cofr front

> alias toggle sel ##display; hide sel models; show ~sel models; ~sel

> alias stoggle sel ##display; hide sel & $1 models; show ~sel & $1 models;
~sel

executed startup.cxc  
UCSF ChimeraX version: 0.91 (2019-08-01)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

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

Opened multi-channel map CHEST CT 4, 4 channels, grid size 512,512,236, pixel
0.576,0.576,1.25, shown at step 1, values int16  

> show #!1.1.1.1.4 models

> hide #!1.1.1.1.4 models

> hide #!1.1.1.1.3 models

> hide #!1.1.1.1.2 models

> show #!1.1.1.1.2 models

> show #!1.1.1.1.3 models

> hide #!1.1.1.1.3 models

> hide #!1.1.1.1.2 models

> ui mousemode rightMode "map eraser"

> hide #!2 models

> show #!2 models

> select #1.1.1.1.1

2 models selected  

> volume erase #1.1.1.1.1 center -56.081,31.571,-113.65 radius 50.888 outside
true

> show #!1.1.1.1.2 models

> show #!1.1.1.1.3 models

> show #!1.1.1.1.4 models

> hide #!2 models

> show #!1.1.1.1.1 models

> view

> view

> hide #!1.1.1.1 models

> view

> view #3

No displayed objects specified.  

> hide #!1.1.1.1.4 models

> hide #!1.1.1.1.3 models

> hide #!1.1.1.1.2 models

> view

> show #!1.1.1.1 models

> hide #!1.1.1.1 models

> show #!1.1.1.1.2 models

> hide #!1.1.1.1.2 models

> hide #!1.1.1.1.1 models

> show #!1.1.1.1.2 models

> show #!1.1.1.1.3 models

> show #!1.1.1.1.4 models

> hide #!3 models

> show #!3 models

> close #3

> volume #1.1.1.1.1 show style image

> toolshed show "Model Panel"

> show #!2 models

> select clear

> hide #!1.1.1.1.2 models

> hide #!1.1.1.1.3 models

> hide #!1.1.1.1.4 models

> hide #!1.1.1.1 models

> show #!1.1.1.1.1 models

> show #!1.1.1.1.2 models

> show #!1.1.1.1.3 models

> show #!1.1.1.1.4 models

> hide #!1.1.1.1.2 models

> hide #!1.1.1.1.3 models

> show #!1.1.1.1.2 models

> show #!1.1.1.1.3 models

> hide #!1.1.1.1.4 models

> hide #!1.1.1.1.3 models

> hide #!1.1.1.1.2 models

> show #!1.1.1.1.2 models

> show #!1.1.1.1.3 models

> show #!1.1.1.1.4 models

> hide #!1.1.1.1.2 models

> hide #!1.1.1.1.3 models

> hide #!1.1.1.1.4 models

> hide #!2 models

> show #!2 models

> show #!1.1.1.1.2 models

> show #!1.1.1.1.3 models

> show #!1.1.1.1.4 models

Can only have one displayed volume when erasing  

> hide #!1.1.1.1.4 models

> hide #!1.1.1.1.3 models

> hide #!1.1.1.1.2 models

> volume erase #1.1.1.1.1 center -53.344,46.531,-121.17 radius 41.3 outside
true

> hide #!3 models

> show #!3 models

> hide #!2 models

> view

> show #!1.1.1.1.1 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!1.1.1.1.1 models

> hide #!2 models

> close #1.1.1.1.2,3,4

> volume settings

Settings for map CHEST CT 4  
grid size = 512 512 236  
region = 0 0 0 to 511 511 235  
step = 2 2 2  
voxel size = 0.576 0.576 1.25  
surface levels = 646.3  
image levels = -228.21,0.015385 76.397,0.87692 360.9,0  
image brightness factor = 1  
image transparency depth = 0.5  
blendOnGpu = False  
boxFaces = False  
btCorrection = False  
capFaces = True  
colorMode = auto8  
colormapOnGpu = True  
colormapSize = 256  
dimTransparency = True  
dimTransparentVoxels = True  
flipNormals = False  
limitVoxelCount = True  
lineThickness = 1.0  
linearInterpolation = True  
maximumIntensityProjection = False  
meshLighting = True  
minimalTextureMemory = False  
orthoplanePositions = (0, 0, 0)  
orthoplanesShown = (False, False, False)  
outlineBoxLinewidth = 1.0  
outlineBoxRgb = (1.0, 1.0, 1.0)  
planeSpacing = min  
projectionMode = 3d  
showOutlineBox = False  
smoothLines = False  
smoothingFactor = 0.3  
smoothingIterations = 2  
squareMesh = True  
subdivideSurface = False  
subdivisionLevels = 1  
surfaceSmoothing = False  
twoSidedLighting = True  
voxelLimit = 7.44875  
  
Settings for map CHEST CT 4 copy  
grid size = 512 512 236  
region = 0 0 0 to 511 511 235  
step = 1 1 1  
voxel size = 0.576 0.576 1.25  
surface levels = 646.3  
image levels = -228.21,0.015385 76.397,0.87692 360.9,0  
image brightness factor = 1  
image transparency depth = 0.5  
blendOnGpu = False  
boxFaces = False  
btCorrection = False  
capFaces = True  
colorMode = auto8  
colormapOnGpu = True  
colormapSize = 256  
dimTransparency = True  
dimTransparentVoxels = True  
flipNormals = False  
limitVoxelCount = True  
lineThickness = 1.0  
linearInterpolation = True  
maximumIntensityProjection = False  
meshLighting = True  
minimalTextureMemory = False  
orthoplanePositions = (0, 0, 0)  
orthoplanesShown = (False, False, False)  
outlineBoxLinewidth = 1.0  
outlineBoxRgb = (1.0, 1.0, 1.0)  
planeSpacing = min  
projectionMode = 3d  
showOutlineBox = False  
smoothLines = False  
smoothingFactor = 0.3  
smoothingIterations = 2  
squareMesh = True  
subdivideSurface = False  
subdivisionLevels = 1  
surfaceSmoothing = False  
twoSidedLighting = True  
voxelLimit = 7.44875  

> hide #!1.1.1.1 models

> show #!1.1.1.1 models

> hide #!3 models

> hide #!1.1.1.1 models

> show #!1.1.1.1 models

> hide #!1.1.1.1 models

> show #!3 models

> save ghostcube.cxs

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 763, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 264, in process  
return copy_state(data, convert=self._add_obj)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 174, in copy_state  
return _copy(data)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 172, in _copy  
return convert(data)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 240, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of SphereModel class in ChimeraX-
MapEraser bundle because the class name is not listed in the name to class
table for session restore  
  
RuntimeError: Unable to restore objects of SphereModel class in ChimeraX-
MapEraser bundle because the class name is not listed in the name to class
table for session restore  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2655, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 213, in export  
result = self.export_func(session, path, **kw)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 763, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 264, in process  
return copy_state(data, convert=self._add_obj)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 174, in copy_state  
return _copy(data)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 172, in _copy  
return convert(data)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 240, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of SphereModel class in ChimeraX-
MapEraser bundle because the class name is not listed in the name to class
table for session restore  
  
RuntimeError: Unable to restore objects of SphereModel class in ChimeraX-
MapEraser bundle because the class name is not listed in the name to class
table for session restore  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by Elaine Meng, 6 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → cannot save session with volume eraser sphere?

comment:2 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Was trying to save eraser sphere model. Made it not save the sphere model. Active mouse modes are not currently saved in session.

Note: See TracTickets for help on using tickets.