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#2450 closed defect (fixed)

Various segmentation problems

Reported by:	jaremko@…	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:        Windows-10-10.0.18362
ChimeraX Version: 0.91 (2019-09-27)
Description
Map segmentation does not group/ungroup properly with selections. Regrouping selected segments will only undo the previous ungroup. 
Also, we can't selective color segments like in Chimera.

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

> ui mousemode rightMode zoom

> lighting soft

> graphics silhouettes true

> hide atoms

> show cartoons

UCSF ChimeraX version: 0.91 (2019-09-27)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r391.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r392.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r401.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r407.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r478.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r487.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1804.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1808.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1836.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1845.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1849.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1856.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1865.mrc
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/job141_run_class001__r1869.mrc

Opened job141_run_class001__r391.mrc, grid size 320,320,320, pixel 1.07, shown
at level 1.58e-06, step 2, values float32  

> volume all step 1

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.4 models

> show #!1.4 models

> hide #!1.5 models

> show #!1.5 models

> hide #!1.7 models

> show #!1.7 models

> hide #!1.7 models

> show #!1.7 models

> hide #!1.8 models

> show #!1.8 models

> hide #!1.9 models

> show #!1.9 models

> hide #!1.9 models

> show #!1.9 models

> hide #!1.11 models

> show #!1.11 models

> close session

> open
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job141/run_class001.mrc

Opened run_class001.mrc, grid size 320,320,320, pixel 1.07, shown at level
0.00453, step 2, values float32  

> surface dust #1

> toolshed show "Segment Map"

Segmenting run_class001.mrc, density threshold 0.008591  
Showing run_class001.seg - 0 regions, 0 surfaces  
Showing 46 region surfaces  
930 watershed regions, grouped to 46 regions  

> hide #!2 models

> show #!2 models

> hide #!1 models

Ungrouped to 3 regions  

> select clear

Ungrouped to 3 regions  

> select clear

Ungrouped to 5 regions  

> select clear

Smoothing and grouping, standard deviation 5 voxels  
Showing 27 region surfaces  
Got 27 regions after smoothing 5 voxels.  
Ungrouped to 39 regions  
Ungrouped to 6 regions  

> color sel red

> select clear

> select clear

> toolshed show "Measure and Color Blobs"

> select clear

> open
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job140/job141_run_DNA-
red.seg

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\ui\gui.py", line 599, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]))  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\models.py", line 637, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\io.py", line 489, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\io.py", line 445, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\segger\segfile.py", line 116, in open_segmentation  
seg = read_segmentation(session, path, open = True)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\segger\segfile.py", line 303, in read_segmentation  
raise ValueError('Segmentation file format is not "segger"')  
ValueError: Segmentation file format is not "segger"  
  
ValueError: Segmentation file format is not "segger"  
  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\segger\segfile.py", line 303, in read_segmentation  
raise ValueError('Segmentation file format is not "segger"')  
  
See log for complete Python traceback.  
  

> select clear

> open
C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/relionnew/Refine3D/job140/job141_run_class001.seg

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\ui\gui.py", line 599, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]))  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\commands\open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\models.py", line 637, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\io.py", line 489, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\core\io.py", line 445, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\segger\segfile.py", line 116, in open_segmentation  
seg = read_segmentation(session, path, open = True)  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\segger\segfile.py", line 303, in read_segmentation  
raise ValueError('Segmentation file format is not "segger"')  
ValueError: Segmentation file format is not "segger"  
  
ValueError: Segmentation file format is not "segger"  
  
File "C:\Program Files\ChimeraX-20190927\bin\lib\site-
packages\chimerax\segger\segfile.py", line 303, in read_segmentation  
raise ValueError('Segmentation file format is not "segger"')  
  
See log for complete Python traceback.  
  

> select clear

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

Smoothing and grouping, standard deviation 5 voxels  
Showing 27 region surfaces  
Got 27 regions after smoothing 5 voxels.  




OpenGL version: 3.3.0 NVIDIA 430.86
OpenGL renderer: GeForce GTX 1050 Ti with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (4)

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 → Various segmentation problems

Reported by Matt Jaremko

comment:2 by Tom Goddard, 6 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed error opening segmentation (.seg) file written by Chimera.
Fixed grouping of selected regions with the Group button.
Fixed coloring of segmentation regions. Can select them and use "color sel blue". I made each region its own surface model, so they also individually appear in Model Panel under the segmentation model.
Fixed saving segmentations.

Thanks for reporting the problems. I ported Segger from Chimera to ChimeraX a few months ago and it was a bigger job than I thought and I ran out of time and obviously didn't test it enough.

in reply to: 3 ; follow-up: 3 comment:3 by jaremko@…, 6 years ago

Great, thanks Tom. Will this be available in the next daily build?

Best,
Matt

-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Friday, September 27, 2019 11:43 PM
Cc: goddard@cgl.ucsf.edu; Jaremko, Matt <jaremko@cshl.edu>
Subject: Re: [ChimeraX] #2450: Various segmentation problems

#2450: Various segmentation problems
----------------------------------+-------------------------
          Reporter:  jaremko@…    |      Owner:  Tom Goddard
              Type:  defect       |     Status:  closed
          Priority:  normal       |  Milestone:
         Component:  Volume Data  |    Version:
        Resolution:  fixed        |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 Fixed error opening segmentation (.seg) file written by Chimera.
 Fixed grouping of selected regions with the Group button.
 Fixed coloring of segmentation regions.  Can select them and use "color  sel blue".  I made each region its own surface model, so they also  individually appear in Model Panel under the segmentation model.
 Fixed saving segmentations.

 Thanks for reporting the problems.  I ported Segger from Chimera to  ChimeraX a few months ago and it was a bigger job than I thought and I ran  out of time and obviously didn't test it enough.

--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_trac_ChimeraX_ticket_2450-23comment-3A2&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=gdGAhEToR6Fy2NsfsCJYDceXTlOUl1KC6Swuu6c-9mM&s=IwmSyNMc8BT9lEB7nSlzKivmYOPUS17MmFF3c27GG0I&e= > ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=gdGAhEToR6Fy2NsfsCJYDceXTlOUl1KC6Swuu6c-9mM&s=xcjaH_Esf5kPcghnsElglmaFj1x9NhYnoLqpErQy4d4&e= > ChimeraX Issue Tracker

in reply to: 4 ; follow-up: 4 comment:4 by goddard@…, 6 years ago

Yes in the current daily build.

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