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FPGA powertrain controls device and drivers: Engine position tracking (EPT) VI not syncing with encoder

Hi all,

Running into blind alleys with my FPGA code. I am trying to use the ept_enc_vte4_revc VI available under powertrain controls device and drivers to read A and Z pulses from my encoder. I am using a NI9411 to read the pulses and a cRIO9149 to interface with host PC. The encoder puts out 720 pulses/rev. In a perfect world EPT VI with all the correct inputs should sync and output the current CAD position as soon as sync command is enabled. However, it didn't work for me and the missed crank/ cam flag lit up. To determine if it's  a signal issue or my code is incorrect, I am simulating square pulses as A and Z pulses. There are no more missed CAM and crank flags now but still it syncs for a fraction of a second and then sync stops. Can't figure out what is wrong with the inputs. Attaching my FPGA and host panel for reference. Any suggestions what I might be missing here?

A few pointers :

The code is now set up for the simulated A and Z pulses. After every 299 A pulses a Z pulse is simulated. Based on the square wave generator set at 5 kHz the EPT VI correctly identifies the engine speed at 1000 rpm. I am using the 2 stroke configurations as the Z pulse is treated as the CAM pulse.

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