AE CC will allow you to isolate areas in the WarpStabilizer. CS5 will not. I do not think that is the right tool for the job.
I took a look at your photos and there's not much there to lock on to. Humor me and read the following story.
I did a similar timelapse project in Glacier park a bunch of years ago. We packed 15 miles in to the wilderness on horseback with a surveyors transit, 4 sacks of concrete and some hardware to set up a mounting base for a movie camera late in August. At the location I did some survey work, checked the sun path tables, made a bunch of calculations, shot some stills and set up a permanent mounting system by pouring concrete and setting mounting studs in the ground so we could return and mount a Mitchell 35MM camera on a set of Baby legs with a motorized geared head and a Tobin motor controller. From my calculations I planned that the camera would shoot 1 frame every 80 seconds from sunrise to sunset tracking the sun across the sky.
Early the next spring, the first time we could get in through the snow we packed in with the camera gear, located our mounting pad, and then spent 2 days doing time lapse. We returned every two weeks until the snow became so deep we could not get back in. We ended up with a boat load of time-lapse footage panning from east to west from sun rise to sun set. The sequences were combined in post so the camera action matched exactly and the seasons changed as we panned across the scene. Starting with a sunrise on a snow covered valley, seeing the wild flowers bloom by the time the sun was 1/4 the way across the sky, then the full glory of summer at the half way point, to leaves turning gold and snow falling at sunset and deep snow at dusk. The shot worked because of planning and accuracy. There was no such thing as camera tracking when I did the shot (1978 - 1979), it was all matched up on an optical bench a frame at a time.
This story brings me to my point, you've picked a very difficult scene with only a few immediate foreground objects to track. The best way to line those objects up would be to use Photoshop's Edit/Auto Align. Portrait photographers use this tool to line up group shots so they can easily replace faces. I gave it a try with a screen cap of 6 of your photos. It works fairly well, but there are slight differences in camera position and angle that make perfect alignment difficult. I'm sure that this will work much better than WarpStabilizer and you can tweak the frames that don't quite match up by hand. Load your Photoshop file as a composition and sequence the layers.
Next time you plan a project like this make sure that there are several areas in the image with constant immobile geometry. We used the ridge line of the distant mountains to pull off the shot I talked about. I wish I had a link to it, but the client has held on to the footage like it was the Hope Diamond.
Interesting. I figured I could lock onto the rocks in the creek, or especially the dam wall in the Big Snapper Pond series, pretty well. Most of the rocks never move, the dam definitely never moves, but are covered in either snow or ice in a handful of frames. I don't mind if those frames are off, I just don't want it to throw the next 40-50 frames out of whack like the Warp does now.
I tried using Photoshop, but it choked: Too many photos in the sequence, not enough RAM. I could break it up and do 100 or so at a time in Photoshop, but it literally took hours for each run, and I don't have that much time. Plus, the alignment between each subset of aligned photos is always off. Also, the process of exporting them back out of photoshop to use in After Effects was really goofy. I'm not just using AE for stabilization, I'm using it to lay in graphics for 10 different weather/time data points.
I hadn't previoulsly turned on the "Detailed Analysis" on the Warp stabilization. When I did, it un-rotated all the photos it had previously rotated (Big Snapper Pond series). From my POV, the alignment still isn't perfect, but it's good enough. I will try this with my Tunnel of Love series too. My 3rd series doesn't have the same 'vegetation heavy' frame edges, there are some fairly immobile trees on either side and a prominent line of rocks all the way across. I haven't had problems with alignment on that series when running tests.
You can see a short sample of what I'm producing here: http://www.youtube.com/watch?v=gR9mlXFdkVE
When I started the project and selected the locations, I didn't realize I'd have so many issues with photo alignment. I never thought about those kinds of issues. I've learned a lot in the process of developing this project over the last year. Had I understood, I would have manually aligned each photo, day by day, frame by frame, and not had this issue at the end.
Thanks for you help, and the fascinating story!
The reason I picked a 35mm Mitchell camera for my project was that you could take a developed frame from a previous shot run it through a frame cutting tool and slide the frame punch into a slot in the camera's optical path. This allowed you to perfectly match up a previous framing by looking through the viewfinder and a transparency of a previous frame for perfect alignment. The feature was introduced in the camera to allow perfect alignment of glass matte paintings and other visual effects in the days where things had to be done by hand.
On each trip I took along frame punches for 10 key camera positions shot on the first trip in. The first day in while setting up the camera and the controller I aligned everything using these frame punches. This meant that each pass was perfectly lined up with the 'master' frames shot months earlier.
If I was shooting this with an electronic camera today I would take along a laptop and use the live feed to line things up in the same way.
As for trying to solve this problem in Photoshop, how many frames do you have? If your finished time lapse is 30 seconds it means about 900 frames or 3 photos a day. The first thing I would do is to run your images through Lightroom and develop them all for uniform density and resize them to a maximum size of just over 4K (about 4500 pixels wide). If your going for HD output I'd size them to about 2500 pixels wide. Batch re-name these images with a sequential number and put 10 to 15 images at a time in a separate folder.
You could then record a Photoshop action that added all of the photos in a folder to a single Photoshop file as new layers and run the Edit/Auto Align to process each folder. Even on a modest computer this operation should only take about 10 minutes per folder. I just tried it on 10 iPhone photos and the entire process took less than 2 minutes on a modest Mac Mini.
You might also want to try using Mocha or AE's point tracker to Stabilize the shots for scale and rotation. Setting the tracker on two rocks or using Mocha to track two tree trunks will probably give you better alignment than Warp stabilizer because there is so little in the frame that really remains the same.
Good luck with your project. I have shot a lot of time lapse in the past, hidden cameras in secure boxes with solar powered battery chargers in the wilderness for weeks at a time. Timelapse is and always be about perfect camera alignment.
The purpose of the project was a lot bigger than just a time lapse at the end. That creek's watershed is our entire downtown. In 2012, the creek was badly damaged by runoff from a fire at a car parts store. The first purpose was just to take and post the photos every day on social media, often with comments about the environment, to drive awareness of creek health and the environment.
I'm not by any stretch a professional photographer, I just like to take pictures. My camera is just a Nikon S4300. I call it "the little camera that could." It's probably taken 50,000+ photographs over the last year as part of this project. That's kind of amazing considering what a POS the previous Nikon camera I had was. It's suffered the most miserable treatment a camera could withstand.
The time lapses at the end were always an idea, but I sure never "planned" for it. I used joist brackets and screws to manufacture camera jigs with a pin in it, thinking I'd get a fairly consistent shot every day. Instead, I learned just how much trees and wood structures move with changes in heat and humidity, just how much play there was putting the camera in the jig. I was facing 3-5 degrees of pitch, yaw. and roll every day. It took me awhile to stabilize the jigs more, and I just kept taking more and more pictures every day, and perpetually adjusting the jigs, until I could usually get one that aligned fairly well
Sites 1 and 3 have acceptable alignment using Warp stabilizer at this point. It's just Site 2 that I'm still having trouble with.
I make my final picture run tomorrow morning, and hope to have the final time lapses finished and uploaded by 5 pm. Then, I'm done.
The only time lapses I'm planning to do next year are one or two "one day" events, with firmly, properly mounted cameras. I do plan to invest in the whole "game cam" type rig with the solar panels and all to achieve this.
I may have to try using Photoshop for my Site 2 pictures. I haven't tried using the extra analysis feature on that photo set yet. We'll see.
Thank you so much for taking the time to correspond with me. You've been very helpful.
Best wishes for a prosperous new year!
One other thing that limited the overall quality of photos for this project, is the fact that I ride a bicycle to work and back every day. The photo sites are on my commute route. My time to take photos was very limited, and I couldn't carry extra equipment every day. I had to do this with nothing but a camera that could fit in my pocket.
It's almost amazing this turned out as well as it did given the circumstances. I'm working on my final time lapse sequences now.
Here's an idea. Avery has transparent printable labels. Print up a bunch of them with your master image, stick one of them to the back of the LCD on your camera and when you get to the location just stand in about the same spot and line up the shot looking through the transparent label.
I'm actually done with the project now, and I'll never try doing the same thing the same way again.
It took me awhile to figure this out (as in like 6 months), but I finally put reference photos on my camera's memory card, so that I could flip back and forth between that and each day's pictures while I was there taking photos, to get better alignment. Still not perfect, but that really improved overall photo alignment. If I were stabilizing just the photos after I implemented that, I probably wouldn't have much problem with image stabilization.
The frame rate of the playback is only 4 frames a second, and even though alignment isn't perfect, it's what I consider "good enough" at that frame rate. This project isn't really photography-centric, it's far more about genral environemental awareness. So, I'm not feeling very anal about the photo alignment at the end.
I've finished my first site's final movie, and have started uploading it already. I'll post the link when it's published on YouTube.
That's quite a project. I thought it was great when somebody moved a big rock on sequence 2...