New answers tagged transparency
I had the same issue with Inkscape/Mac OS/LaTeX. I was able to deal with this by rasterizing only the problematic parts of the image and leaving the rest vectorized. To do this I opened the SVG file selected the object(s) in question in Inkscape and did Edit -- >Make a Bitmap Copy, and then saved as PDF. I couldn't get anywhere on this issue with Inkscape ...
The problem appears to be related to the transparency of the PNG and PDF graphics I was using. I solved the problem by flattening the PDF graphics before inserting them, and opening the PNG files in gimp to remove the alpha channel from those files. (It would appear that pdflatex is invisibly spreading the transparent layer of transparent graphics across ...
I would use ghostscript to remove the transparency once the pdf is generated, using gs -o converted.pdf -sDEVICE=pdfwrite -dHaveTransparency=false input_file.pdf
I just had the same problem. If your figure is not too complex, you can also solve this by changing the order in which you display things (think of a "Send to Back" option), so you can mimic transparency. So in your example, instead of using the opacity option, just fill with fill = black!50 which is 50% black, and make sure you put your rectangle before ...
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