Allow 2dlabel to place images in scene

[e.emmott@…]

Begin forwarded message:

From: "Emmott, Ed"
Subject: [chimerax-users] 2dimage?
Date: January 31, 2018 at 11:15:24 AM PST
To: "chimerax-users@…"

Hi,
Is there (or likely to be in future) a 2d image feature, allowing you to overlay 2d graphics (.tif, .png) in the same way as the 2dlabel command (e.g. Xpos Ypos )? My use case is wanting to add additional 2d graphics (e.g. color bar or graphs) over a pdb structure prior to rendering images/generating movies.

Whilst I can get ChimeraX to open the images easily e.g. (open “…test.tif”), they are acquiring edges (white background image on white background scene -> grey borders) I assume as a result of being interpreted as a 3d object. Otherwise loving the software!
Thanks a lot,
Ed

Using ChimeraX build v0.5 (2018-01-12)

Dr Edward Emmott
Research Associate
Slavov Lab
Northeastern University
332 Mugar, 360 Huntington Ave.
Boston, MA.

[Tom Goddard]

ChimeraX does not have a 2d image label capability. When you open a 2D TIFF or PNG it is treating it as a 3d density map with one plane -- this is a bad way to try to insert a 2D image, the brightness profile won't even be linear, transparency will be used instead of having an opaque image, the gray one pixel edge border is probably unintentional.

For adding color bars and graphs to 2d images the most common approach is to do this in an image editor, not in ChimeraX. Same for movies, use a movie editor. ChimeraX is not intended to replace Photoshop and Final Cut. That said, our 2d text labels are just images in the graphics and it would not be especially hard to add 2d image labels. But we have hundreds of other features we are trying to get into ChimeraX and I think this is a low priority (although I'm about to hack exactly this kind of feature in today for multi-person virtual reality ChimeraX sessions to show a picture of each person's face in the scene -- but won't be accessible as a general command which is 20 times more work).

[e.emmott@…]

Thank you for the quick response. I admit my use case is not completely normal as otherwise as you suggest adding the image afterwards in photoshop/iMovie etc is standard. In my case I am using a matlab script to write chimeraX command files based off mass spectrometry data. If there was a chimeraX  function then this is something I can include in the pipeline. I am trying to avoid hands on manipulation steps as from a throughput perspective this wouldn't really be doable.

I completely understand there's other features which are more urgent, and thanks again for the great piece of software!
Best,
Ed


-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Wednesday, January 31, 2018 3:52 PM
Cc: Emmott, Ed <e.emmott@northeastern.edu>; goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #1018: Allow 2dlabel to place images in scene

#1018: Allow 2dlabel to place images in scene
----------------------------------+----------------------
          Reporter:  e.emmott@…   |      Owner:  goddard
              Type:  enhancement  |     Status:  assigned
          Priority:  moderate     |  Milestone:
         Component:  Depiction    |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+----------------------

Comment (by goddard):

 ChimeraX does not have a 2d image label capability.  When you open a 2D  TIFF or PNG it is treating it as a 3d density map with one plane -- this  is a bad way to try to insert a 2D image, the brightness profile won't  even be linear, transparency will be used instead of having an opaque  image, the gray one pixel edge border is probably unintentional.

   For adding color bars and graphs to 2d images the most common approach  is to do this in an image editor, not in ChimeraX.  Same for movies, use a  movie editor.  ChimeraX is not intended to replace Photoshop and Final  Cut.  That said, our 2d text labels are just images in the graphics and it  would not be especially hard to add 2d image labels.  But we have hundreds  of other features we are trying to get into ChimeraX and I think this is a  low priority (although I'm about to hack exactly this kind of feature in  today for multi-person virtual reality ChimeraX sessions to show a picture  of each person's face in the scene -- but won't be accessible as a general  command which is 20 times more work).

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1018#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

Seems like this would be my responsibility.

This request has been partially addressed in that the "key" command can place color keys on the image.