every floppy disk has a test pin used to perform drive alignment. this pin is connected to an oscilloscope to see the raw, analog output of the head amplifiers. this analog signal is processed by the drive's filters and edge detection circuits to generate the digital flux pulses seen at the read data lines.
your project uses an an oscilloscope to grab this data; this sharply complicates the capture of real analog data.
I've got one of these oscilloscopes, but it's not clear how to rig this all together.