I am curious about this error and if it is a problem when trying to get the highest speed performance.
The waves peak at 8 per second, which is the same as the rotation rate here. The back shaft of the stepper motor is flush with the housing so I had to drill a 1/4" coaxial hole and press a pin to hold the encoder disc. The hole is off center a few thousandths. Projecting out that far from the lathe collect it was hard to get perfection.
ch0->InputMode=ENCODER_MODE;
ch0->OutputMode=CL_MICROSTEP_MODE;
ch0->Vel=400;
ch0->Accel=3000;
ch0->Jerk=80000;
ch0->P=0;
ch0->I=0.0017;
ch0->D=0;
ch0->FFAccel=0;
ch0->FFVel=0.0005;
ch0->MaxI=10000;
ch0->MaxErr=1e+009;
ch0->MaxOutput=10000;
ch0->DeadBandGain=1;
ch0->DeadBandRange=0;
ch0->InputChan0=12;
ch0->InputChan1=0;
ch0->OutputChan0=8;
ch0->OutputChan1=9;
ch0->MasterAxis=-1;
ch0->LimitSwitchOptions=0x100;
ch0->LimitSwitchNegBit=0;
ch0->LimitSwitchPosBit=0;
ch0->SoftLimitPos=1e+006;
ch0->SoftLimitNeg=-1e+006;
ch0->InputGain0=-0.025;
ch0->InputGain1=1;
ch0->InputOffset0=0;
ch0->InputOffset1=0;
ch0->OutputGain=1;
ch0->OutputOffset=0;
ch0->SlaveGain=1;
ch0->BacklashMode=BACKLASH_OFF;
ch0->BacklashAmount=0;
ch0->BacklashRate=0;
ch0->invDistPerCycle=-1;
ch0->Lead=0;
ch0->MaxFollowingError=1000;
ch0->StepperAmplitude=204;
ch0->iir[0].B0=1;
ch0->iir[0].B1=0;
ch0->iir[0].B2=0;
ch0->iir[0].A1=0;
ch0->iir[0].A2=0;
ch0->iir[1].B0=1;
ch0->iir[1].B1=0;
ch0->iir[1].B2=0;
ch0->iir[1].A1=0;
ch0->iir[1].A2=0;
ch0->iir[2].B0=1;
ch0->iir[2].B1=0;
ch0->iir[2].B2=0;
ch0->iir[2].A1=0;
ch0->iir[2].A2=0;
