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#3137 closed defect (fixed)

SeggerX and save dialog need updating

Reported by:	jaremko@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Input/Output	Version:
Keywords:		Cc:	pett
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: 0.93 (2020-04-03)
Description
Cannot save segmentation regions from the volume>segment map feature

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "C:\Users\mattj\Google Drive\CSHL\papers\x108\figures\fig4\ORC-
> dna_orientation.cxs" format session

Log from Mon May 4 14:35:38 2020

> ui mousemode rightMode zoom

> set bgColor white

> hide all atoms

> show all cartoons

> color /a #55c087

> color /b #ffe255

> color /c #f6986c

> color /d #6b80bc

> color /e #aa7fba

> lighting soft

> lighting depthCue false

> cartoon suppressBackboneDisplay false

> graphics silhouettes true

UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\mattj\\\Google
> Drive\\\CSHL\\\papers\\\x108\\\figures\\\fig4\\\ORC-dna_orientation.cxs"

opened ChimeraX session  

> close session

> open "C:\Users\mattj\Google Drive\CSHL\papers\x108\figures\fig4\ORC-
> dna_orientation.cxs"

opened ChimeraX session  

> 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 #!1.2 models

> volume #1.1 level 0.008997

> surface dust all

> hide #!1.1 models

> show #!1.2 models

> volume #1.2 level 0.009721

> hide #!1.2 models

> show #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> volume #1.1 level 0.01048

> surface dust all

> volume #1.1 level 0.01059

> show #!1.2 models

> hide #!1.2 models

> view list

Named views: dna-conforms  

> hide #!1.1 models

> show #!1.2 models

Expected an objects specifier or a view name or a keyword  

> save session "C:/Users/mattj/Google Drive/CSHL/papers/x108/figures/fig4/ORC-
> dna_orientation.cxs"

> toolshed show "Segment Map"

> hide #!1.2 models

> show #!1.1 models

Segmenting run_it025_class001.mrc, density threshold 0.010587  
Showing run_it025_class001.seg - 0 regions, 0 surfaces  
Showing 47 region surfaces  
937 watershed regions, grouped to 47 regions  
Ungrouped to 4 regions  

> select clear

Ungrouped to 4 regions  

> select clear

Ungrouped to 13 regions, but did not show all surfaces, see Options  

> select clear

Ungrouped to 17 regions, but did not show all surfaces, see Options  

> select clear

> select #1.1

2 models selected  

> select clear

> select #1.1

2 models selected  

> hide #!2 models

> show #!2 models

Smoothing and grouping, standard deviation 5 voxels  
Showing 25 region surfaces  
Got 25 regions after smoothing 5 voxels.  
Ungrouped to 36 regions  
Grouped 5 regions  

> color sel red

Grouped 55 regions  

> color sel #b2b2b2

> view list

Named views: dna-conforms  

> view dna-conforms

> select clear

> hide #!2 models

> view dna-conforms

> select clear

> hide #!1.1 models

> show #!1.1 models

> toolshed show "Show Volume Menu"

> save session "C:/Users/mattj/Google Drive/CSHL/papers/x108/figures/fig4/ORC-
> dna_orientation.cxs"

Summary of feedback from opening C:\Users\mattj\Google
Drive\CSHL\papers\x108\figures\fig4\ORC-dna_orientation.cxs  
---  
note | Showing run_it025_class001.seg - 2 regions, 2 surfaces  
  
opened ChimeraX session  

> hide #!2 models

Segmenting run_it025_class003.mrc, density threshold 0.009721  
Showing run_it025_class003.seg - 0 regions, 0 surfaces  
Showing 47 region surfaces  
811 watershed regions, grouped to 47 regions  

> hide #!2 models

> show #!2 models

Ungrouped to 4 regions  

> select clear

Ungrouped to 3 regions  

> select clear

Ungrouped to 7 regions  

> select clear

> select clear

Ungrouped to 4 regions  

> select clear

Grouped 6 regions  
Grouped 55 regions  

> color sel #b2b2b2

> color sel red

> select clear

> view list

Named views: dna-conforms  

> view dna-conforms

> hide #!2 models

> surface dust all

> save session "C:/Users/mattj/Google Drive/CSHL/papers/x108/figures/fig4/ORC-
> dna_orientation.cxs"

> surface dust all

> volume all hide

> volume #1.1 show

> volume #1.1 level 0.0106

> view dna-conforms

> hide #!1.1 models

> show #!1.2 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1156, in SaveSegmentation  
self.SaveSegmentationAs()  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1156, in SaveSegmentation  
self.SaveSegmentationAs()  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  

> show #!2 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1156, in SaveSegmentation  
self.SaveSegmentationAs()  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  

> hide #!2 models

> save image "C:/Users/mattj/Google Drive/CSHL/papers/x108/figures/fig4/ORC-
> dna_orientation2.png" width 2000 supersample 4 transparentBackground true

> hide #!1.2 models

> show #!1.1 models

> toolshed show "Segment Map"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segment_dialog.py", line 1167, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
AttributeError: 'MainWindow' object has no attribute 'save_dialog'  
  
File "C:\Program Files\ChimeraX_20200403\bin\lib\site-
packages\chimerax\segger\segfile.py", line 172, in show_save_dialog  
sd = mw.save_dialog  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 442.92
OpenGL renderer: GeForce GTX 1050 Ti with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20MFCTO1WW
OS: Microsoft Windows 10 Pro (Build 18362)
Memory: 33,922,240,512
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8850H CPU @ 2.60GHz"

Change History (5)

comment:1 by pett, 5 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Input/Output
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → SeggerX and save dialog need updating

Hi Matt,

Until we get this fixed, you will need to use the "save" command directly to save segmentations, e.g.:

save ~/Desktop/region4.seg models #2

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by Tom Goddard, 5 years ago

Updated Segger to use new open/save APIs for segmentation files.

The Segger "Save As..." menu entry wants to show the save dialog with format menu set to Segmentation and with an initial directory, initial file name, and initial model option, like so (from segger/segfile.py)

show_save_file_dialog(seg.session, format = 'Segmentation', initial_directory = idir, initial_file = ifile, model = seg)

but those options are not supported by the new show_save_file_dialog(). Could probably omit the model argument.

Once Eric add arguments to show_save_file_dialog() I can update Segger to use them.

in reply to: 3 ; follow-up: 3 comment:3 by jaremko@…, 5 years ago

Hi Eric and Tom,

Thanks for the help. I have no problem with using the command line; I just didn’t think of it.

Best,
Matt

-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Tuesday, May 5, 2020 6:04 PM
Cc: goddard@cgl.ucsf.edu; Jaremko, Matt <jaremko@cshl.edu>; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #3137: SeggerX and save dialog need updating

#3137: SeggerX and save dialog need updating
-----------------------------------+----------------------------
          Reporter:  jaremko@…     |      Owner:  Eric Pettersen
              Type:  defect        |     Status:  accepted
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:                |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+----------------------------

Comment (by Tom Goddard):

 Updated Segger to use new open/save APIs for segmentation files.

 The Segger "Save As..." menu entry wants to show the save dialog with  format menu set to Segmentation and with an initial directory, initial  file name, and initial model option, like so (from segger/segfile.py)

      show_save_file_dialog(seg.session, format = 'Segmentation',  initial_directory = idir, initial_file = ifile, model = seg)

 but those options are not supported by the new show_save_file_dialog().
 Could probably omit the model argument.

 Once Eric add arguments to show_save_file_dialog() I can update Segger to  use them.

--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_trac_ChimeraX_ticket_3137-23comment-3A2&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=42ow00O1S4OgunC8qaVtls8wMyZy2NI5E8_MYtOL-qI&s=emOHyI9oA5nInWYAVWZeoWw_uQofiibrsMVNlAyB7pE&e= > ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=42ow00O1S4OgunC8qaVtls8wMyZy2NI5E8_MYtOL-qI&s=MLPA6H37PcPbNbJKDiyeqlskyCg0tE8oidoFcNYKvAk&e= > ChimeraX Issue Tracker

comment:4 by pett, 5 years ago

Cc:	pett added; Tom Goddard removed
Owner:	changed from pett to Tom Goddard
Status:	accepted → assigned

Okay, showing the save dialog now supports the same keywords as it's predecessor, except for 'model'. If you really need it, say so and I'll try to figure something out.

comment:5 by Tom Goddard, 5 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

Ok, the Segger File / Save... menu now sets the Save dialog format to segmentation and the initial directory.

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