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Jeez, it's too bad it's a physical model and not in a 3D application.
You may want to consider the part of the model that eclipses the engines & glows: it will need to be rotoed on a layer above them, and it will need a little light wrap (or reduced-size glow) to help sell it. Not an especially easy task on the first go.
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I just tracked the headlights of this car as it goes through fog in Mocha to see if I could recreate your issue. While the position and anchor point tracks seemed to track nicely, the scale got thrown off when it went through the fog and I had to add a couple manual keyframes to fix it:
Even then the scale of the Null Object woud jump a bit as it went through the fog. In your case you may need to to two different tracks, one up until the light is eclipsed by the ship and one after it comes out from behind the model. Also Dave is probably right about Rotoing out the part of the ship you want in front of the lights.
In my case I was able to fix the scale change in After Effects since the car is moving at a relatively steady speed in this shot. I simply setup up some manual keyframes and used an expression pick whip to match the percentage of the light's Cone Angle to the percentage of the Scale. If you're curious here's how I set it up:
A) I copied and pasted the Anchor Point, Position, Rotation and Scale data from Mocha onto my Null. Since The anchor point and position were the only bits of data that I needed for the shot, I deleted the others including rotation and scale which I fixed with some manual keyframes do to the steady motion of the vehicle.
B) Then I manually set the anchor of my Null layer to 0 so that the corner matched the center of the headlight.
C) Then I added two lights, an ambient light and a spot light, and I parented the spot light to the Null Object. (This may work differently with Video Copilot Optical Flares, but my understanding is that they use lights as well so it might actually be pretty similar)
D) Then I option clicked on the Spot Light's Cone Angle to create an expression and I pick whipped the scale property of the Null object. Now the light's Cone Angle will change to match the scale of the Null Object.
E) Finally I fiddled with the Scale keyframes and ended up having it start at 30% and finish at 60%.
I almost had a heart attack this morning, when I came to the office, I saw the one of the new models for the first time. It is about a hands lenght, and split into 4 moveable segments. It can curl into a little ball. I have heard talk about it, and from what I have heard, this model will be filmed and composited as a little flying drone. My poor nerves!
Thanks for the input, I will try it out, and see what I can come up with. As mentioned, the standard tracking in After Effects, and Mocha do a pretty good job, and at the moment I use manual keyframes to fix the bits and pieces, and since the Video CoPilot lens flares work quite well with other layers, selling the effect of the glow moving behind is not too bad. But thank you for the mention on the light-wrap. I have my "save the noobs" list of "Must have's" on a post-it stuck to my monitor. This includes things like - Motion Blur, Easy-easy etc, But I forgot the light wrap! Ill add it now, cause that really will make a nice difference.
Well, wish me luck (as you wave me goodbye) and hopefully I can even put an example online in the near future.
Thank you for the tips. At the moment, I create a point light to attach to the null I have tracked. You are correct, because in the Optical Flares settings, I then set the flare to track lights. What makes this a great feature, is that I can create as many nulls as I need, just duplicate the point light, position them and attach them to the new nulls, and the lens flare is automatically duplicated and attached to the new light.
I am going to spend the day reading more and more on Mocha, and even the standard tracker in After Effects. I feel pretty comfortable with tracking, but think I need a refresher course! especially to get better at determining which part of the model I should track, how large an area etc etc. Also, learning more about scale and perspective tracking might be a good thing.
Well, after the next few days, hopefully I will be able to give some good feedback.
Thanks again for the screenshot, I will use the suggestion on scaling and rotation (if needed) and see where it gets me.
Here is a nice short clip I found on Youtube. I like the tracking that was done here - looks pretty precise to me. I will see if the author is willing to share some secrets!