Thursday, December 9th, 2010, 1:01 pm
Creating Animations With GNU Octave and the GNU Image Manipulation Program
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he GIMP is an extremely powerful program and animation in the GIMP can be achieved with layers. That’s why I can get so much work done just with Free software and GNU tools like gnuplot. This includes some of the following new examples, which are done by taking screenshots (from the GIMP), stacking them up as layers, and then saving them as a GIF file with the animation option enabled.
The following file, an animated GIF image which comprises 8 frames with 600ms setting them apart (click the image to zoom), shows my new algorithm tracking the heart’s boundaries in a sequence taken from the same slice, which prevents sudden, unregistered change in the intensity values near the point being probed. 16 points are initially fixed in a region, equally spaced although that is not a strict requirement because the program takes any list of points and handles each one in turn. The points are separated by a 5-pixel distance in the x and y axes although that too can vary independently based on parameter input that sets a grid (better initialisation would look for edges of interest). The shown arrows are narrow and crude although an option exists for making them thick (which then hides interesting parts of the image). The shuffle parameters in this case involve a frame size of 9×9 pixels, a shuffle radius of 5 pixels, and a summation of pixel-wise differences.
A colour representation of the same images sequence is shown below (click to zoom).
Another newly-implemented method looks at another measure for a window of pixels taken from consecutive frames. It considers a minimum of pixel-wise differences in a given range rather than take the average difference. The results obtained using each of these methods cannot be easily compared without a simplified synthetic set and a proper study would need to involve systematic experiments that look at how varying window size, radius, and calculation method affects overall performance. There is quite a project right there, but it only involves tracking, with or without tagging. Tags can help in identifying good landmark points to start with — points that define an anatomically-meaningful edge to start from and track as the sequence of frames progresses. Eventually, providing a formula for normalising a measure of similarity would be nice. Such a normalisation method — if properly applied — gives a new way of finding landmark points ‘on the move’. Doing so using non-rigid registration (NRR) is not possible for the heart as there is hardly a one-to-one correspondence between points (too much movement). The hope is that by employing a fast tracking algorithm with a good transform which adjusts itself for image intensity, size et cetera, it will be possible to identify edges and perform localised measurements, perhaps even do statistical analysis based on different sets of videos (long-term goal). These ideas are not far fetched and the body of work already done in this area ought to be explored. The novelty is the transform being used to quickly calculate similarity wrt neighbouring points, so existing work look at how to adjust parameters so as to get better results. In this particular problem domain, tracking the heart’s contours reliably and robustly enough is the objective, however it is not simple to do this ‘on he fly’ (speed of video playback for example).
December 10th, 2010 at 12:43 am
Automate your animation with ffmpeg or memcoder. I’ve used the instructions here with some success:
http://electron.mit.edu/~gsteele/ffmpeg/
This page is similar.
http://www.comanswer.com/question/ffmpeg-how-to-i-set-the-images-sequence-to-be-equal-to-the-duration-of-the-movie-with
You might also try to automate your image annotation with image magic. Gnuplot can be used to generate sequential plots of your data by script then annotation added and finally the sequence animated without too much trouble.
December 10th, 2010 at 8:03 am
Can the “animate” command in ImageMagick achieve this too? Will it allow the user to output to file? Can it stitch files up? For movie-to-image conversion I use avidemux. To be honest, I don’t make animated GIFs so often, so I didn’t look into many options. I’ll see what’s in your links.
December 10th, 2010 at 8:07 am
OK, I’ve looked into it all and bookmarked it. It’s handy, but I still can’t automate movie creation. Back in the days of MATLAB I wrote an extensive GUI which then invoked my callback functions to create a video automatically from each simulation. I’ll have to revisit that code of mine.
April 9th, 2012 at 12:39 am
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