frequency domain tuning with digital components

Hello,
In my company I work daily with digital servos and pc based motion controllers. Up till now it was common to tune our servos in time
domain resulting in a lot of trial and error procedures and non-optimal tuned servos.
I want to shift more to frequency domain tuning, so we can learn more from our systems and know what bandwidths and phase margins we have.
I know how to implement this kind of tuning in a experimental setup with a frequency analyser that adds some noise into the loop between controller and plant and measure the open loop frequency response. But that was with an analog amplifier and the possibility to inject noise into the loop.
Who can help me with a setup based on a digital drive that reads an incremental encoder signal, the reference profile is in the drive (trapezoid) and the drive outputs three pwm signals to drive a brushless dc motor.
Where and how can I add noise? Where and how can I measure a signal in the loop, between controller and amplifier this is not possible? Is it possible to inject the noise on the incremental encoder signal, are there any tools for this purpose? Are there any spectrum analysers that can read an incremental encoder signal?
Does anybody know some interesting literature to learn more on frequency domain tuning with digital servos? Especially the practics?
Mark
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Oldchatterman wrote:

Do you own the software, or are you using 3rd-party software? If you're using your own software & hardware I'd suggest building in some primitive noise generation and data capture facilities into your software (assuming you have the memory for it) and analyzing the results in MatLab or one of the free equivalents.
Failing that you could make a board that could be interposed between your encoder and the rest of the system that would add a digital summing junction -- you could even do it with analog outputs if you wanted to.
--

Tim Wescott
Wescott Design Services
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I don't own the software, because I am using 3rd-party software. As a matter of fact we have a lot of problems to obtain the exact controller structure and gain scalings from this party. I had the wish to identify my controller using an identified plant.
Do you have suggestions for the hardware setup, analog or digital?
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