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Measurement error in reading Encoder Pulses

I am using PCI-6601 card to read a Linear Encoder which gives 2000 pulses per mm of distance.The accuracy of the Linear encoder is 2Microns.In my application I am measuring a distance of 7mm.But the card is reading with an error of 30 to 50 Microns error.We had checked up all the factors related to mechanical and Encoder.In fact the same application was earlier working with Advantech Encoder card which has provisons to connect the A,B,A Bar,B Bar inputs from Encoder.There was an accuracy of 0 to 5Microns.But the application was replaced with NI Card because of the continuous problem of the Digital I/O Card used from Advantech.
Mail me the possible causes and also the troubleshooting procedures for correcting the above problem
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I too, am using linear encoders with a counter card. When error such as yours occurs, your should list all possible causes. In using linear encoders, mechanical play should be checked first. linear encoders, require no mechanical play in all directions, including 90 deg. to the direction of measurement. Next, I would check that you are not measuring this 7mm distance at a rate that exceeds your card input frequency, and your application program. You should also, If you have not done this yet, add a timer to you program that polls your card at a rate similar to your maximum desired needs. Another possible cause could be line noise, in your  connections. Make sure your cables are properly sheided, and grounded, and not located near strong electrical magnet fields. You can also change your encoding level to a lower level i.e. X4 to X2.
 
Good luck!
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