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1- How can I access to source codes of the GUI file (BoardTestSystem.exe)?
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You won't be able to.
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2- Is it possible to capture data from FPGA to PC through USB.2 and save it by making a new windows file?
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Yes. If you have a JTAG connector, you can implement JTAG communications per this tutorial:
http://www.alterawiki.com/wiki/using_the_usb-blaster_as_an_sopc/qsys_avalon-mm_master_tutorial However, JTAG is not particularly fast. If you need to transfer a lot of data, and your board has an ethernet connector, then you might be better off looking at implementing a NIOS II processor on the board with an ethernet connection to your PC. Altera provide example designs.
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3- Can I use bts_ddr2top project to develop FPGA codes and change these codes to match my plan?
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Yes. However, what I would typically do is extract the FPGA pin assignments from the provided example designs for your board, review the schematic, and create my own top-level design. Then re-implement the ddr2top design using the Quartus GUI and MegaWizard IP. To determine what was used in bts_ddr2top, open the project in Quartus and then open the MegaWizard, and make a note of the DDR2 settings.
Doing it this way provides you with the insight needed to build your own HDL code from scratch.
Cheers,
Dave