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Are you expected to manually set registers in Keil µVision?

In the university we had to programm all registers manually. You were only given the header file for the device with all of the registers. From what I have understood Keil acts like an interface to set registers via the CMSIS files. Still some registers are not available in the RTE_Device.h or system.c

So are you expected to set registers manually or not? Does it depend on the device? This is really confusing

For example:

There is the Periphals Menu where you can set all registers while debugging, but I don't see a menu where I can set this before debugging. If I have to set this manually, it is okay, but then I don't know why you can set some registers and not all of them.

I want to configure the hardware timer of the LPC1769. Usually you would set the registers manually. How does Keil access this register? Via the SysTick Timer configuration?