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I have made a crystal structure for my thesis in illustrator. I used a half circle to generate nice spheres using Illustrator's 3D effect:
Now the problem is that the filesize is huge: 40MB when saved as PDF (the format i am importing in to Latex), 25MB as .ai and a little less for an svg. How can I get a decent file size? Is there a way to 'rasterize' the 3D effect or compress it somehow?
What do you mean by 3D effect? You could always just create those spheres by placing a radial gradient inside a circular path. This would be the simplest method to do this.
John's and Andrew's answers are both completely valid, but here's a third option that has a bit of a different workflow.
You have three different spheres which you've presumably copy and pasted repeatedly. When done that way, Illustrator won't recognize that when saving and won't make any optimizations to reduce your filesize.
The way to force Illustrator to make that optimization is to use Symbols. Instead of copy and pasting the spheres, create a symbol for each. You can then copy and paste the Symbol repeatedly. Even with "Preserve Illustrator Editing Capabilities" checked, your filesize will be drastically reduced. I tested it with a few hundred spheres, the file dropped from 45 MB to 568 KB.
You can go John's way but I would also look into the settings when you're exporting to a PDF.
I created a simple document filled with 3D squares. I then exported as a .ai file.
I then saved the same file as a PDF. I made sure to unckeck "Preserve Illustrator Editing Capabilities".
My file output
This should create a much smaller file size than your working Illustrator file.
