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That will depends on what the PIOs are doing. If they are static, then sure you can just read them. In your earlier posts, you commented you wanted to read toggling signals. In that case, you really need to capture them first, eg., into on-chip RAM, or into SDRAM, and then read them out via JTAG. This is pretty much what SignalTap II does (with the samples stored in on-chip RAM). If you cannot figure out how to trigger SignalTap II correctly, then you'll probably having trouble getting this scheme to work too.
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I'm not English so I think I miss some subtlety in the words and I'm not sure I understand it correctly: the signals are coming from a fifo. Is it correct to say they're static? Or how can I manage it?
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I gave you a link to a tutorial back in Post#35.
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I should have read it too quickly, I'll read it again and more carefully...
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