The resolution of 0.1 Hz does require a 10 seconds long acquisition, but instead of running only one sine tone at a time you may consider generating and acquiring multiple tones (eventually all 1000) at once.
This techique of multi-tone excitation / acquisition is very efficient but has some drawbacks.
1 - You system under test has to 'work' under such an excitation signal. This is not always the case.
2 - What you gain in measurement speed, you partially loose in dynamic range. The more tones you use for a measurement the more you 'loose' dynamic since given a total signal range, each tone will have to have a reduced amplitude in order to not overload your system.
3 - The technique requires an Arbitrary Waveform Generator and I don't know if that i
s what you are using.
The setup is a little tricky because the tones have to be an exact multiple of the 0.1 Hz and your acquisition length and sample clock need to be perfectly locked to the generation to avoid frequency domain leakage between the different signals.
On the measurement side use either the Power Spectrum (signel channel) or the Frequency Response (dual channel measurement) but do NOT use a window (= none or = rectangular)
LabVIEW has all the tools needed to help you build that measurement. Check out the Basic Multitone.vi in your Analyze>>Waveform Generation palette.
If everything works for you, you may be able to reduce your measurement time from hours to less than a minute (possibly all the way down to 10 sec. !)
