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#2351 closed defect (fixed)

volume eraser: output array is read-only

Reported by:	yazan.abbas@…	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:        Linux-4.15.0-58-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-08-20)
Description
Was trying to erase small regions of density from a volume that was generated by the volume zone command

Log:
UCSF ChimeraX version: 0.91 (2019-08-20)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/yazan/Dropbox/Abbas_etal_2019_brainV-
ATPase/Figures/Figure2/figure2_6.cxs

opened ChimeraX session  

> windowsize 1800 1800

> view list

Named views: ABpairs, ADP1, ADP1234, ADP2, ADP3, ADPcloseup3, ADPcloseup4,
EGcloseup1, EGcloseup2, EGcloseup2_2, EGcloseup2_3, mutsSIDE, mutsSIDE2,
mutstop, overall1, overall2, slice1  

> view ADPcloseup4

> hide #!10 models

> hide #!9 models

> surface dust #12,16-18 size 10

> show #!1 models

> hide #!16 models

> hide #!1 models

> show #!1 models

> show adp target abp

> set silhouetteDepthJump 0.03

> show #!16 models

> hide #!16 models

> surface dust #12,16-18 size 10

> hide #!11 models

> show #!10 models

> hide #!10 models

> show #!9 models

> hide #!18 models

> hide #!9 models

> show #!10 models

> show #!17 models

> hide #!10 models

> show #!11 models

> hide #!17 models

> toolshed show "Side View"

> clip off

> save session /home/yazan/Dropbox/Abbas_etal_2019_brainV-
ATPase/Figures/Figure2/figure2_6.cxs

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36755, resource id:
29519822, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36756, resource id:
29519822, major code: 25 (SendEvent), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36760, resource id:
29519829, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36761, resource id:
29519829, major code: 25 (SendEvent), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36765, resource id:
29519836, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36766, resource id:
29519836, major code: 25 (SendEvent), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36769, resource id:
29519843, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36770, resource id:
29519843, major code: 25 (SendEvent), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36774, resource id:
29519850, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 36775, resource id:
29519850, major code: 25 (SendEvent), minor code: 0  

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> ui mousemode rightMode "map eraser"

> volume erase #16 center 205.27,149.99,145.23 radius 4.411

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 308, in _erase_in_sphere  
self._erase()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 327, in _erase  
run(self.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 2688, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 24, in volume_erase  
_zero_data_in_sphere(v.data, cvol, radius)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
ValueError: output array is read-only  
  
ValueError: output array is read-only  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
  
See log for complete Python traceback.  
  

> volume erase #16 center 205.27,149.99,145.23 radius 4.411

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 308, in _erase_in_sphere  
self._erase()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 327, in _erase  
run(self.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 2688, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 24, in volume_erase  
_zero_data_in_sphere(v.data, cvol, radius)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
ValueError: output array is read-only  
  
ValueError: output array is read-only  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
  
See log for complete Python traceback.  
  

> volume erase #16 center 204.46,149.93,144.85 radius 4.411

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 308, in _erase_in_sphere  
self._erase()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 327, in _erase  
run(self.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 2688, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 24, in volume_erase  
_zero_data_in_sphere(v.data, cvol, radius)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
ValueError: output array is read-only  
  
ValueError: output array is read-only  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
  
See log for complete Python traceback.  
  

> volume erase #16 center 204.46,149.93,144.85 radius 4.411

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 308, in _erase_in_sphere  
self._erase()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 327, in _erase  
run(self.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 2688, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 24, in volume_erase  
_zero_data_in_sphere(v.data, cvol, radius)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
ValueError: output array is read-only  
  
ValueError: output array is read-only  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.56
OpenGL renderer: GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 6 years ago

Component:	Unassigned → Volume Data
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → volume eraser: output array is read-only

comment:2 by Tom Goddard, 6 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

Session restore of a map whose array is included in the session file restored the map with an unwritable array. The array was produced from a buffer which was apparently not writable. The buffer was from gzip.decompress().

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