Tracking settings in batch processing?

[Jennifer Bussell]

Hi guys,

We're currently batch processing a large number of videos in Ctrax and can't seem to figure out how to load in tracking settings we've optimized from one of the videos. The only options for the arena, fly shape parameters, and background model seem to be "Auto-detect in each movie" or "Use settings from first movie." We'd like to use settings from an already tracked movie, but the batch processor only asks from the movie file itself for the first movie, not an annotation file or anything.

Does anyone know how to load non-automatic tracking settings into the batch processor?

Thanks!

--Jen

[John Bender]

Hi Jen,

I believe the "use settings from first movie" function will load all
the relevant settings from that movie if an annotation file exists for
it with the default name. If it's not doing that, it's probably a bug.
Am I interpreting your question correctly? It's not too hard to add a
"use settings file" option, which would load a separate ann-file with
settings (the same functionality as File->Load settings). Would that
be better?

JB

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[Jennifer Bussell Schiff]

Hi John,

I think a "use settings file" option would be more self-explanatory. Am I understanding correctly that the first movie for batch processing should either be already tracked or have an annotation file created with custom settings but no tracking? Then does it re-track that first video? Does it just look for the .ann file with the default name in the same directory as the first movie?

Thanks for the quick response!

--Jen

--

---------------------------------------------------------------------

Jennifer J. Bussell
Graduate Fellow
Laboratory of Neurogenetics and Behavior
The Rockefeller University
1230 York Avenue Campus Box 63
NY, NY 10065
T 212-327-7237 F 212-327-7238

[John Bender]

Hi Jen,

Yes, yes, and yes. When you put it that way, maybe it does make more
sense to use a separate settings file. But on the other hand, how do
you know your settings are any good if you haven't tracked a movie
with them? Retracking the first movie is a little redundant, but if
you're leaving it overnight anyway...

Well, it's not too hard to add a "use settings file" option, if it
makes things more straightforward. I'm actually fiddling with the
batch window this week already, so I might be able to have this
feature implemented fairly soon.

JB

[Jennifer Bussell Schiff]

Hi John,

Yeah, it seems silly to retrack a movie. In our case, we have a stationary setup where we're filming many batches of movies. We've already tracked a couple of them individually to optimize the tracking settings. So those settings for our setup should work over all of the batches, but we don't want to have to retrack a "starter" movie every night we set up batch processing. A "use settings file" option would be great for us!

Will try tonight loading settings from an old file into a new annotation file for a new movie but not tracking it until it's added as the first movie in a batch process. That should work, right?

[John Bender]

Hi Jen,

I'm not sure exactly when the settings are saved into the new
annotation file (upon load or upon track). I'm pretty sure that if you
open a new movie, load the settings, start tracking, then stop
tracking, it will save the settings to the new movie's annotation
file. Then you can make that movie the first in your batch and "use
settings from first movie".

JB

On Thu, Jun 28, 2012 at 1:23 PM, Jennifer Bussell Schiff

[John Bender]

Hi Jen,

The "use settings file" option is included in Ctrax 0.3.5, in addition
to some other revamping of the batch-processing functionality.

JB

On Thu, Jun 28, 2012 at 1:23 PM, Jennifer Bussell Schiff