File content as of revision 1:3d22d4e6de38:

// reference this code http://www.fmf.uni-lj.si/~ponikvar/STM32F407%20project/Timer2_Counting.pdf
#include "mbed.h"
#include "stm32f4xx.h"

int main(){
 RCC->AHB1ENR |= 0x01 + 0x10; // Clock for PortA, E
 RCC->APB1ENR |= 0x01; // Clock for Timer2
 GPIOA->MODER |= 0x00000008; // all inputs but: PA1 => AF mode
 GPIOA->AFR[0] |= 0x00000010; // select AF1 (TIM2) for PA01 -> TIM2_CH2

 TIM2->CCMR1 |= 0x0100; // Ch. 2 as TI2
 TIM2->SMCR |= 0x0007; // Ext. clk mode 1
 TIM2->SMCR |= 0x0060; // TI2FP2 as ext. clock
 TIM2->CR1 |= 0x0001; // enable counting

 while (1) {
        int16_t count1;
        count1=TIM2->CNT; 

        printf("%d\r\n", count1);
        wait(1.0);
 if (GPIOE->IDR & 0x01) TIM2->CNT = 0; // reset counter
 if (GPIOE->IDR & 0x02) TIM2->CR1 |= 0x01; // enable counter
 if (GPIOE->IDR & 0x04) TIM2->CR1 &= ~0x01; // disable counter
 };
}