[chimerax-users] 4D imaging - metadata and time slider

[Tom Goddard]

Hi Mateusz,

  I see the map series slider doesn’t appear because some code change disabled showing the slider.  I’ve fixed that — fix is in tonight’s daily build.

  In the meantime you can use the vseries command to show the slider (for map series #1):

	vseries slider #1

Here is the ChimeraX vseries command documentation

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/vseries.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/vseries.html>

  For labeling the images with the tiime you can use the 2dlabel command.  For a saving a single presentation image you can just type the 2dlabel command with the needed time value.  But I guess you want the case where you record a movie.  For that you can use the “perframe” command to update the label at each frame,  for example, command

   perframe "2dlabel change tlabel text $1" range 0,107.5 frames 50 format %.2f

changes the text once per frame for 50 frames cover time range 0-107.5.  In a movie recording script you would use this with the vseries command have the times update as the movie plays

	movie record
	vseries play #1
        perframe "2dlabel change tlabel text $1" range 0,107.5 frames 50 format %.2f
        wait 50
	movie encode ~/Desktop/mymovie.mp4

Put those commands in a text file with suffix *.cxc (ChimeraX commands) and open it to record the movie.  Or you can put all 5 of those commands on one line separated by semicolons to record the movie.

  I’m improving the 3d light microscopy, time series and multichannel handling every week, so let me know when I’ve broken things.

	Tom


> On Aug 23, 2017, at 3:44 AM, Mateusz Biesaga <mateusz.biesaga at gmail.com> wrote:
> 
> Hi all,
> 
> I use ChimeraX for 4D visualization and so far I am very satisfied with the results, thank you for this amazing tool! I have a two questions:
> 
>  - While presenting data that changes in time (xyt or xyzt as I do in Chimera) it is usually required to display the timing on the image. Is there a way to access the metadata and display it, possibly using 2dlabels function? I work particularly with TIFF files.
> 
> - After I upgraded Chimera to second alpha release, I can see no time slider above the command line. I open my 4D data using asterisk in the filename, as described in tutorial:
> http://www.rbvi.ucsf.edu/chimera/data/light-apr2017/light4d.html <http://www.rbvi.ucsf.edu/chimera/data/light-apr2017/light4d.html>
> Is there a new way of accessing this slider?
> 
> Thanks,
> Mateusz
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