Anthony,
Thanks for the fast response. Forgive my ignorance, but I'm not sure what you mean when you talk about just wanting the shape.
Basically, this is what I'm trying to accomplish. I have a directory of .eps clip art files. I have a program that is taking arbitrary user-selected images from here and resizing them, changing the color, and converting to a raster format which can then be included in an SVG document. Since the clip art images can be overlapping, it's important that the transparent parts of each image are preserved.
The first step the program takes is to convert the clipart from a .eps file into a grayscale .png file. Using this command:
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convert clip1.eps -colorspace gray -resize 200x200 newclip.png
Then I do a gradient table lookup to color the clip art with the user-specified color:
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convert -colorspace RGB -size 10x100 gradient:#ff0000-#ffffff gradient.png
convert newclip.png gradient.png -fx 'v.p{0,u*v.h}' finalclip.png
All of this works perfectly, except that the transparent regions of the .eps files become opaque white, and thus each subsequent clip art image covers whatever images are below it instead of having see-through portions.
I hope all of that was clear.