Sound Card
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Leave the Setup dialog open and from the Menu RUN NaP3 in Expanded.
The Configure button allows the chosen device to be set up appropriately. For a sound card with separate input channels (rather than a stereo pair) it runs the bargraph balance meter at the bottom of the tab. The card input controls should be set so that the centre green LED is lit most of the time (OK, you can settle for a few either side!). A ~S9 signal source is best but it can be set with empty band noise.
With the FUNCube Dongle Pro Plus it will open a dialog to set appropriate values (see the FUNCube DP+ section below).

The Set Gain button will show a level control to adjust the display calibration with the card set externally for optimum performance. This ensures that the incoming signals do not exceed the NaP3 headroom.
 
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                                               Balance shown at bottom                                              Level Control

Leave the Setup dialog open and RUN NaP3 in Expanded. Feed an S9 signal to your rig and set it to CW with ~600Hz bandwidth. A calibrated signal source connected to your antenna (like the Elecraft XG2) is now (and later) really useful, but if your rig can locate any steady signal close to S9 on your rig meter with any preamp switched in and no attenuator, tune it into the passband. Adjust the Level slider until the NaP3 S meter reads S9 (-73dBm). Do not worry about any other part of the display.
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To set the noise floor on a band hover the mouse cursor above the Avg button and adjust the noise floor with the mouse wheel, for the Waterfall a hover over Peak will act similarly. These will be saved per band, as will many other settings. More, much more, on this and other NaP3 functions can be found in this Help file, but you should now be well set up to explore further. Information on many controls can be seen by hovering the mouse cursor over the control. When this gets annoying just check Disable Tool Tips in the Options tab.
If your card has little inherent balance or you have problems with your connections you may see signal images. Images are identical mirror images either side of the centre as shown in the first picture below. The second shows the display after the NaP3 image cancellation routine is set up as described in the Menu/Configure/DSP section of this Help file.
 
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If images persist, your sound card may still need to balance the left and right inputs correctly, or you are feeding a mono signal to both card inputs, or a lead is not making a proper connection. You can wait for the automatic wideband image rejection to learn values for your hardware - a strong broadcast signal in the passband will allow this. Or see the Menu/Configure/DSP section in this Help file for more information on other methods of setting WBIR.
If the display 'tunes the wrong way' you have your inputs swapped. NaP3 expects the I signal in the Left channel and Q on the Right. A quick way to change this is the IQ Swap checkbox in the Input tab.