Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#3779 closed defect (fixed)

chimerax.segger.segcmd.export_mask: 'Place' object is not subscriptable

Reported by: dherreros@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: gregdp@…, Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-48-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Saving a segger segmentation with function "export_mask" imported from "chimerax.segger.segcmd" returns the following error:

TypeError                                 Traceback (most recent call last)
<ipython-input-5-d60153fe17b6> in <module>
----> 1 export_mask(smod, savePath='/home/davidherreros/mask.mrc')

~/scipion3/software/em/chimerax-1.1/lib/python3.7/site-packages/chimerax/segger/segcmd.py in export_mask(segmentation, savePath, format, binSize, sequentialIds)
    280 
    281     m = segmentation.mask
--> 282     origin = segmentation.grid_origin()
    283     step = segmentation.grid_step()
    284 

~/scipion3/software/em/chimerax-1.1/lib/python3.7/site-packages/chimerax/segger/regions.py in grid_origin(self)
     66 
     67         tf = self.point_transform()
---> 68         return tuple([tf[a][3] for a in (0,1,2)])
     69 
     70     def grid_step(self):

~/scipion3/software/em/chimerax-1.1/lib/python3.7/site-packages/chimerax/segger/regions.py in <listcomp>(.0)
     66 
     67         tf = self.point_transform()
---> 68         return tuple([tf[a][3] for a in (0,1,2)])
     69 
     70     def grid_step(self):

TypeError: 'Place' object is not subscriptable

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 266, in _strptime  
month = _months.index(month_name)  
ValueError: tuple.index(x): x not in tuple  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 342, in initialize  
api._api_caller.initialize(api, session, self)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1265, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 38, in nag  
_check_usage(session)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 192, in _check_usage  
usage = _get_usage()  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 228, in _get_usage  
usage["dates"].append(_strptime(value))  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 275, in _strptime  
raise ValueError("time data does not match format")  
ValueError: time data does not match format  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/davidherreros/mask.seg format segger

Summary of feedback from opening /home/davidherreros/mask.seg  
---  
note | Showing 4 region surfaces  
  
Traceback (most recent call last):  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 629, in customEvent  
func(*args, **kw)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer  
cxcmd(session, topic)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd  
run(session, cmd)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 188, in provider_open  
session.models.add(opened_models)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/models.py", line 641, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model mask.seg #2 to scene twice  
  
ValueError: Attempted to add model mask.seg #2 to scene twice  
  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/models.py", line 641, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  
Showing mask.seg - 4 regions, 4 surfaces  

> ui tool show Shell

/home/davidherreros/scipion3/software/em/chimerax-1.1/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")  




OpenGL version: 3.3.0 NVIDIA 450.66
OpenGL renderer: GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Alienware
Model: Alienware m15 R2
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        6.9G        3.4G        416M        5.1G        7.8G
	Swap:          5.6G          0B        5.6G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e9b]	
	Subsystem: Dell Device [1028:093b]	
	Kernel driver in use: i915
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    pyzmq: 19.0.2
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    sfftk-rw: 0.6.6.dev0
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    Sphinx: 3.1.1
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    urllib3: 1.25.10
    wcwidth: 0.2.5
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    wheel: 0.34.2

Change History (8)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → chimerax.segger.segcmd.export_mask: 'Place' object is not subscriptable

Reported by David Herreros

comment:2 by Tom Goddard, 5 years ago

Cc: gregdp@… added

The first error of the 3 in your log is from trying to call export_mask() from Python. It appears you directly called this Python function from the Python shell. Unfortunately Segger has not been entirely ported to ChimeraX (from Chimera originally). If a capability is not available from the graphical user interface it almost surely has not been ported. The code is about 30,000 lines written by Greg Pintilie and I spent a week porting it but that only got through the most common features. The error is typical of differences between Chimera 1 and ChimeraX.

Second error is ChimeraX registration code, and third error is opening saved segmentation, both the same as your previous bug report #3778.

comment:3 by Tom Goddard, 5 years ago

Cc: Elaine Meng added
Resolution: → fixed
Status: assigned → closed

Fixed.

I ported the the Segger export mask command, e.g. "segger exportmask #2 save mask.mrc". The command has the same syntax as the Chimera "segment exportmask" command. I renamed it to "segger" because ChimeraX already has a different segment command. Refer to the Chimera "segment exportmask" docs for details. The documentation will be added to ChimeraX shortly. I did not port any of the other segment subcommands.

The other two errors, startup registration error, and opening .seg file were fixed as part of bug #3778.

in reply to:  5 ; comment:5 by dherreros@…, 5 years ago 

Good morning Tom,

Thank you so much for all your help. I have downloaded the daily build 
of ChimeraX and the error related to #3778 appears to be solved.

However, I am trying to use the new "segger exportmask #2" command and 
ChimeraX reports that it doesn't exists. Am I doing something wrong? Is 
there a way to update Segger to get the latest fixes?.

Again, thank you for all your help and time.

Kind regards,

David Herreros

On 2/10/20 5:20, ChimeraX wrote:

in reply to:  6 ; comment:6 by goddard@…, 5 years ago 

Oops!  Forgot to upload the new segger code with the segger exportmask command.  Done now.  Tonight's ChimeraX build will have it.

in reply to:  7 ; comment:7 by dherreros@…, 5 years ago 

Good morning Tom,

I have tried the new daily build of ChimeraX and everything works fine know.

Thank you so much for all your help.

Kind regards,

David Herreros

On 5/10/20 19:53, ChimeraX wrote:

in reply to:  8 ; comment:8 by goddard@…, 5 years ago 

Good!  Thanks for reporting the problem.  Helps us improve ChimeraX.
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