Opened 6 years ago

Closed 6 years ago

#2482 closed defect (fixed)

Save Segger segmentation: 'MainSaveDialog' object has no attribute '_file_dialog'

Reported by: krey.thomas@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-21)
Description
Tried to save a segmentation file, which caused an error (and I guess the segmentation was not saved).

Log:
UCSF ChimeraX version: 0.91 (2019-09-21)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/tkrey/Desktop/3bvl.pdb

3bvl.pdb title:  
Structural basis for the iron uptake mechanism of helicobacter pylori ferritin
[more info...]  
  
Chain information for 3bvl.pdb #1  
---  
Chain | Description  
A B C D E F | ferritin  
  
Non-standard residues in 3bvl.pdb #1  
---  
FE — Fe (III) ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  

> close session

> open /Users/tkrey/Desktop/emd_20430.map

Opened emd_20430.map, grid size 720,720,720, pixel 2.06, shown at step 1,
values float32  

> volume region all orthoplanes off

> toolshed show "Marker Placement"

> toolshed show "Map Eraser"

> select clear

> select #1

3 models selected  

> select clear

> volume erase #1 center 745.64,749.43,220.37 radius 249.96 outside true

> toolshed show "Map Eraser"

> hide #!2 models

> hide #!4 models

> surface dust #3 size 100

> surface dust #3 size 200

> select clear

> select #3

2 models selected  

> view sel

> select clear

> hide #!4 models

> select #3

2 models selected  

> toolshed show "Side View"

> toolshed show "Side View"

> view sel

> select clear

> save session
/Users/tkrey/Desktop/Thomas/Documents/Paper/2019/2019_CVSC/figures/figure_3_pentamer_curvature/20191008/KSHV_C1_portal_cap.cxs

> toolshed show "Volume Viewer"

> toolshed show "Volume Viewer"

> save session
/Users/tkrey/Desktop/Thomas/Documents/Paper/2019/2019_CVSC/figures/figure_3_pentamer_curvature/20191008/KSHV_C1_portal_cap_selected.cxs

> toolshed show "Segment Map"

Segmenting emd_20430.map copy, density threshold 0.002706  
Showing emd_20430 copy.seg - 0 regions, 0 surfaces  
Only showing 500 of 5479 regions.  
Showing 500 of 5479 region surfaces  
Only showing 500 of 671 regions.  
Showing 500 of 671 region surfaces  
5479 watershed regions, grouped to 671 regions  

> select clear

> select clear

Segmenting emd_20430.map copy, density threshold 0.002706  
Showing emd_20430 copy.seg - 0 regions, 0 surfaces  
Only showing 500 of 5479 regions.  
Showing 500 of 5479 region surfaces  
Showing 104 region surfaces  
5479 watershed regions, grouped to 104 regions  
Ungrouped to 2 regions  
Ungrouped to 3 regions  
Smoothing and grouping, standard deviation 7 voxels  
Showing 80 region surfaces  
Got 80 regions after smoothing 7 voxels.  
Ungrouped to 3 regions  
Smoothing and grouping, standard deviation 8 voxels  
Showing 66 region surfaces  
Got 66 regions after smoothing 8 voxels.  
Ungrouped to 2 regions  
Ungrouped to 4 regions  
Smoothing and grouping, standard deviation 9 voxels  
Showing 54 region surfaces  
Got 54 regions after smoothing 9 voxels.  
Ungrouped to 26 regions  
Got 42 regions after grouping by connections  
Ungrouped to 2 regions  
Ungrouped to 2 regions  
Ungrouped to 2 regions  
Ungrouped to 2 regions  
Got 29 regions after grouping by connections  
Got 20 regions after grouping by connections  
selected regions have 2 total sub regions  

> select clear

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segfile.py", line 172, in show_save_dialog  
initial_directory = idir, initial_file = ifile, model = seg)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 108, in display  
fd = self._file_dialog  
AttributeError: 'MainSaveDialog' object has no attribute '_file_dialog'  
  
AttributeError: 'MainSaveDialog' object has no attribute '_file_dialog'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 108, in display  
fd = self._file_dialog  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segfile.py", line 172, in show_save_dialog  
initial_directory = idir, initial_file = ifile, model = seg)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 108, in display  
fd = self._file_dialog  
AttributeError: 'MainSaveDialog' object has no attribute '_file_dialog'  
  
AttributeError: 'MainSaveDialog' object has no attribute '_file_dialog'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 108, in display  
fd = self._file_dialog  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segment_dialog.py", line 1156, in SaveSegmentation  
self.SaveSegmentationAs()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segfile.py", line 172, in show_save_dialog  
initial_directory = idir, initial_file = ifile, model = seg)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 108, in display  
fd = self._file_dialog  
AttributeError: 'MainSaveDialog' object has no attribute '_file_dialog'  
  
AttributeError: 'MainSaveDialog' object has no attribute '_file_dialog'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 108, in display  
fd = self._file_dialog  
  
See log for complete Python traceback.  
  

> save session
/Users/tkrey/Desktop/Thomas/Documents/Paper/2019/2019_CVSC/figures/figure_3_pentamer_curvature/20191008/KSHV_C1_portal_cap_selected.cxs

Segmenting emd_20430.map copy, density threshold 0.002706  
Showing emd_20430 copy.seg - 0 regions, 0 surfaces  
Only showing 500 of 5479 regions.  
Showing 500 of 5479 region surfaces  
Showing 177 region surfaces  
5479 watershed regions, grouped to 177 regions  
Showing 177 region surfaces  
Segmenting emd_20430.map copy, density threshold 0.002706  
Showing emd_20430 copy.seg - 0 regions, 0 surfaces  
Only showing 500 of 5479 regions.  
Showing 500 of 5479 region surfaces  
Showing 104 region surfaces  
5479 watershed regions, grouped to 104 regions  
Ungrouped to 2 regions  
Ungrouped to 2 regions  
Ungrouped to 2 regions  
Ungrouped to 3 regions  
Smoothing and grouping, standard deviation 7 voxels  
Showing 80 region surfaces  
Got 80 regions after smoothing 7 voxels.  
Ungrouped to 4 regions  
Ungrouped to 2 regions  
Got 51 regions after grouping by connections  
Ungrouped to 2 regions  
Ungrouped to 2 regions  
Got 34 regions after grouping by connections  
Got 23 regions after grouping by connections  
Ungrouped to 2 regions  
Ungrouped to 2 regions  
Got 19 regions after grouping by connections  

> vop gaussian #3 sdev 6.18

> select #5

2 models selected  

> select clear

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/segfile.py", line 172, in show_save_dialog  
initial_directory = idir, initial_file = ifile, model = seg)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 108, in display  
fd = self._file_dialog  
AttributeError: 'MainSaveDialog' object has no attribute '_file_dialog'  
  
AttributeError: 'MainSaveDialog' object has no attribute '_file_dialog'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 108, in display  
fd = self._file_dialog  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-1.68.22
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by pett, 6 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Save Segger segmentation: 'MainSaveDialog' object has no attribute '_file_dialog'

comment:2 by pett, 6 years ago

Resolution: → fixed
Status: assigned → closed

Hi Thomas,

This bug was fixed about 6 days after the version you downloaded, so if you download the current daily build you should be okay, Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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