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The ADC is for an audio application so the output rate will be quite high. What I need to do first for my project is perform an offset correction and determine the frequency at the input(fast).
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In that case, you need to consider the signal processing separate from the NIOS processor. The processor can be used to configure the signal processing path, and to read results, but it would not be involved in processing of individual samples.
What does 'offset correction' entail? Measuring the DC value of the signal, and then adjusting it until it is zero, or simply removing the DC component?
Start by getting a simple example working first, eg., the DC offset, or perhaps the input power, and then work on the frequency estimation.
You should also try and implement the software equivalent of the processing of the samples in a signal processing package like MATLAB. Its much simpler to develop algorithms and look at spectra in MATLAB, and then decide what needs to be implemented in hardware.
Cheers,
Dave