Opened 6 years ago
Closed 6 years ago
#2596 closed defect (fixed)
Problem with BlobOutlineBox in sessions
Reported by: | 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: Linux-4.15.0-70-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.91 (2019-11-20) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-11-20) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/storage/Experiments/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Roi001.cxs" format session opened ChimeraX session > open "/storage/Experiments/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Roi002.cxs" format session opened ChimeraX session > toolshed show "Command Line Interface" > toolshed show "Measure and Color Blobs" > toolshed show "Volume Viewer" > toolshed show "Map Coordinates" > measure blob #!4.1 triangleNumber 131194 color #0000ccff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #4.1 blob: volume = 0.0038812 area = 0.15588 size = 0.28461 0.20828 0.18151 > measure blob #!4.1 triangleNumber 132715 color #9d08c9ff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #4.1 blob: volume = 0.0038812 area = 0.15588 size = 0.28461 0.20828 0.18151 > measure blob #!4.1 triangleNumber 107521 color #35ef49ff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #4.1 blob: volume = 0.0038812 area = 0.15588 size = 0.28461 0.20828 0.18151 > measure blob #!4.1 triangleNumber 237218 color #da4d6cff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #4.1 blob: volume = 0.0038812 area = 0.15588 size = 0.28461 0.20828 0.18151 > volume #4 step 2 > volume #4 step 4 > volume #4 step 8 > show #!3 models > show #3.1 models > close #3 > close #4 > ui autostart true "Volume Viewer" > ui autostart true "Measure and Color Blobs" > toolshed show "File History" > open "/storage/Experiments/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Recs TS Tiles (xy4z4)/Roi002_C1_N1_clath650-syn560_3D_561_5,17K_(15968,14000)_TS3D.tif" Opened Roi002_C1_N1_clath650-syn560_3D_561_5,17K_(15968,14000)_TS3D.tif, grid size 750,750,300, pixel 0.004, shown at step 4, values float32 > open "/storage/Experiments/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Recs TS Tiles (xy4z4)/Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif" Opened Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif, grid size 750,750,300, pixel 0.004, shown at step 4, values float32 > toolshed show Shell /usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn("IPython History requires SQLite, your history will not be saved") > toolshed show "Volume Viewer" > volume #2 > volume #3 > measure blob #!2.2 triangleNumber 8015 color #ab1abcff outline true Surface Roi002_C1_N1_clath650-syn560_3D_561_5,17K_(15968,14000)_TS3D.tif #2.2 blob: volume = 0.00062001 area = 0.043841 size = 0.16266 0.10204 0.10971 > volume showOutlineBox true > hide #!2 models > ~select #1 Nothing selected > volume #2 step 8 > volume #2 step 4 > volume #3 step 8 > volume #3 level 0.003 > volume #3 change image level 0,0 level 0.003179,0.8 level 0.04172,1 color #c17d11 color #c17d11 color #c17d11 > volume #3 level 0.004 > volume #3 level 0.002 > volume #3 level 0.001 > volume #3 level 0.002 > volume #3 level 0.003 > volume #3 step 16 > volume #3 level 0.0035 > volume #3 level 0.002 > volume #3 step 8 > volume #3 level 0.004 > volume #3 step 4 > volume #!3 step 1 > volume #!3 step 2 > volume #!3 step 1 > volume #3 level 0.008 > volume #3 level 0.01 > volume #3 step 2 > volume #3 step 4 > volume #3 level 0.001 > volume #3 level 0.005 > volume #3 step 8 > volume #3 step 16 > volume #3 step 4 > volume #3 level 0.008 > volume #3 level 0.001 > volume #3 step 1 > volume #3 step 2 > volume #3 step 4 > volume #3 level 0.005 > volume #3 level 0.01 > volume #3 step 8 > volume #3 step 4 > volume #3 level 0.005 > volume #3 level 0.01 > volume #3 level 0.001 > volume #3 step 8 > volume #3 step 4 > volume #3 step 8 > volume #3 level 0.005 > volume #3 level 0.003 > volume #3 level 0.0025 > volume #3 level 0.003 > volume #3 level 0.004 > volume #3 level 0.003 > volume #3 level 0.005 > volume #3 level 0.004 > volume #3 level 0.003531 > volume #3 level 0.004 > volume #3 level 0.005 > volume #3 step 4 > volume #3 level 0.006154 > volume #3 level 0.008693 > volume #3 level 0.005058 > volume #3 level 0.008116 > volume #3 step 8 > volume #3 level 0.003 > volume #3 level 0.004 > volume #3 level 0.003 > save session "/home/flo/ExperimentsHDD/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Roi002.cxs" > volume #2 level 0.0003 > volume #2 change image level 0,0 level 0.000344,0.8 level 0.03739,1 color #555753 color #555753 color #555753 > open "/storage/Experiments/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Recs TS Tiles (xy4z4)/Roi002_C1_N1_clath650-syn560_3D_561_5,17K_(15968,14000)_TS3D.tif" Opened Roi002_C1_N1_clath650-syn560_3D_561_5,17K_(15968,14000)_TS3D.tif, grid size 750,750,300, pixel 0.004, shown at step 4, values float32 > volume #2 > volume #2 level 0.003 > volume #2 change image level 0,0 level 0.000344,0.8 level 0.03739,1 color #555753 color #555753 color #555753 > volume #2 level 0.0374 > volume #2 level 0.03 > volume #2 level 0.0374 > volume #2 level 0.003 > open "/storage/Experiments/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Recs TS Tiles (xy4z4)/Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif" Opened Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif, grid size 750,750,300, pixel 0.004, shown at step 4, values float32 > volume #2 > volume showOutlineBox true > volume #2 step 8 > open "/storage/Experiments/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Recs TS Tiles (xy4z4)/Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif" Opened Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif, grid size 750,750,300, pixel 0.004, shown at step 4, values float32 > volume #2 step 8 > volume #2 > volume #2 level 0.00318 > volume #2 change image level 0,0 level 0.003179,0.8 level 0.04172,1 > volume showOutlineBox true > save session "/home/flo/ExperimentsHDD/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Roi002.cxs" > vop gaussian #2 sdev 0.012 > volume #2 change image color #f57900 color #f57900 color #f57900 > volume #3 step 2 > volume #3 step 4 > volume #3 step 8 > volume #3 step 4 > volume #3 step 2 > volume #3 step 4 > volume #3 step 2 > volume #3 step 1 > volume #3 step 2 > volume #3 step 4 > volume #3 step 8 > volume #3 step 4 > volume #3 step 1 > volume #3 step 2 > volume #3 step 1 > volume #3 step 2 > volume #3 step 4 > vop gaussian #3 sdev 0.012 > volume #4 step 4 > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!4 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > show #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > show #!2 models > hide #!3 models > hide #!4 models > volume #2 level 0.004 > volume #2 level 0.005 > vop gaussian #2 sdev 0.012 > show #!2 models > hide #!2 models > volume #5 step 4 > show #!2 models > hide #!5 models > volume #5 step 8 > volume #5 step 4 > close #5 > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > close #3 > close #4 > volume #2 level 0.006 > volume #2 level 0.005 > vop gaussian #2 sdev 0.012 > volume #3 step 4 > volume #2 level 0.00318 > volume #2 level 0.005 > volume #2 level 0.00318 > show #2.1 models > hide #2.2 models > show #2.2 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > close #3 > vop gaussian #2 sdev 0.012 > volume #3 level -4.996e-18,0 level 0.002805,0.8 level 0.02513,1 > volume #3 > open "/storage/Experiments/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Recs TS Tiles (xy4z4)/Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif" Opened Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif, grid size 750,750,300, pixel 0.004, shown at step 4, values float32 > volume #2 level 0.005 > hide #!3 models > volume #4 > volume #4 style image > volume #4 maximumIntensityProjection true > volume #4 region 0,0,148,749,749,148 step 1 maximumIntensityProjection false showOutlineBox true > volume #4 region 0,0,0,749,749,299 step 4 > volume #4 region 0,0,0,749,749,299 step 1 colorMode opaque8 orthoplanes xyz positionPlanes 374,374,149 > volume #4 orthoplanes off boxFaces true > volume #4 style surface region 0,0,0,749,749,299 step 4 colorMode auto8 boxFaces false > volume #4 step 8 > volume #4 level 0.005 > volume #4 change image level 0,0 level 0.003179,0.8 level 0.04172,1 > volume #4 step 4 > volume #4 step 2 > volume #4 step 8 > volume #4 step 16 > volume #4 step 8 > vop gaussian #4 sdev 0.012 > volume #5 step 4 > volume #5 step 8 > volume #5 step 16 > volume #5 step 4 > volume #3 step 4 > show #!3 models > hide #!5 models > show #!5 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!5 models > close #4-5 > open "/storage/Experiments/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Recs TS Tiles (xy4z4)/Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif" Opened Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif, grid size 750,750,300, pixel 0.004, shown at step 4, values float32 > volume #4 > volume #4 step 8 > volume #4 step 16 > volume #!4 showOutlineBox true > vop gaussian #4 sdev 0.012 > volume #5 step 4 > volume #5 step 1 > volume #3 change image color #cc0000 color #cc0000 color #cc0000 > close #4-5 > show #!3 models > volume #3 step 8 > volume #3 region 0,0,0,749,749,299 > ui mousemode rightMode "pick blobs" > measure blob #!3.2 triangleNumber 4337 color #1717fdff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #3.2 blob: volume = 0.0058596 area = 0.23202 size = 0.3258 0.29639 0.26297 > select #3 4 models selected > ~select #3.2 3 models selected > select #3.1 1 model selected > select #3 4 models selected > select #3 4 models selected > select #3 4 models selected > ~select #3.2 3 models selected > ~select #3.3 2 models selected > select #3.1 1 model selected > select #3 4 models selected > select #3 4 models selected > select #3.1 1 model selected > select #3 4 models selected > select #3 4 models selected > select #3 4 models selected > select #2 3 models selected > select #3.3 1 model selected > select #3 4 models selected > select #3 4 models selected > ~select #3.2 3 models selected > select #3.1 1 model selected > select #3.3 1 model selected > ~select #3.3 Nothing selected > show #3.1 models > hide #3.1 models > hide #3.2 models > show #3.2 models > toolshed show "Measure and Color Blobs" > toolshed show "Map Eraser" > close #4 > volume #3 step 4 > toolshed show "Basic Actions" > select #3.2 1 model selected > select clear > select #3 3 models selected > toolshed show "Model Panel" > toolshed show "Side View" > toolshed show "Measure and Color Blobs" > ~select #3.2 2 models selected > close #4 > toolshed show "Measure and Color Blobs" > close #4 > ui mousemode rightMode "pick blobs" > measure blob #!3.2 triangleNumber 235 color #7ed441ff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #3.2 blob: volume = 0.0076333 area = 0.27692 size = 0.34982 0.32344 0.25447 > measure blob #!3.2 triangleNumber 101 color #7c7bb9ff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #3.2 blob: volume = 0.0049626 area = 0.17786 size = 0.32631 0.25185 0.15787 > measure blob #!3.2 triangleNumber 3495 color #d64976ff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #3.2 blob: volume = 0.0038641 area = 0.15163 size = 0.28076 0.20578 0.18085 > measure blob #!3.2 triangleNumber 14004 color #e56f16ff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #3.2 blob: volume = 0.0061409 area = 0.25293 size = 0.32661 0.2894 0.27176 > measure blob #!3.2 triangleNumber 57919 color #8f27cfff outline true Surface Roi002_C1_N1_clath650-syn560_3D_647_17,03K_(15968,14000)_TS3D.tif gaussian #3.2 blob: volume = 0.0046307 area = 0.22697 size = 0.40864 0.2561 0.18726 > save session "/home/flo/ExperimentsHDD/CLAP/161205 CLAP#2 (div9 clat syn PAINT)/Roi002.cxs" Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 794, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 206, in _copy return convert(data) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax-daily/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 BlobOutlineBox class in ChimeraX- PickBlobs bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of BlobOutlineBox class in ChimeraX- PickBlobs bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py", line 910, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py", line 640, in file_save_cb self.save_dialog.display(self, session) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py", line 139, in display fmt.save(session, filename) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 1098, in save run(session, cmd) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2837, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 990, in save_session save(session, filename, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py", line 220, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 794, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/state.py", line 206, in _copy return convert(data) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax-daily/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 BlobOutlineBox class in ChimeraX- PickBlobs bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of BlobOutlineBox class in ChimeraX- PickBlobs bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax-daily/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. QXcbConnection: XCB error: 3 (BadWindow), sequence: 45280, resource id: 9765380, major code: 40 (TranslateCoords), minor code: 0 OpenGL version: 3.3.0 NVIDIA 435.21 OpenGL renderer: GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
Component: | Unassigned → Sessions |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Problem with BlobOutlineBox in sessions |
comment:2 by , 6 years ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
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Fixed.
Pick blob outline box model did not have session saving support.