The third day we came in we decided to completely revamp our controller to LabVIEW. We first connected analog in and analog out pins to the same low pass filter we set-up the day before. Next, we created a .vi that simulated a signal of random white noise voltage out to the circuit. We also programmed the .vi to accept and write input voltages from the capacitor in the circuit. Then, we wrote each input and output voltage into a measurement .txt file. Finally, we were able to pass this data into Matlab where we ran the tfestimate command and were able to obtain somewhat reasonable results. The low pass filter results of can be seen in the figure below.

Note that the data does not fit well with the expected response. The cut off frequency and the dc gain agree well, but the roll off rate is significantly higher than expected. Hours were spent trying to track down the bug. Sampling rate, number of samples, resistors, capacitors were all varied and this was the best response we were able to generate. After exhausting all of our resources and spending several hours changing random parameters our team decided to table this aspect of the project and seek assistance from our instructors.
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