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TIM2 Configuration as up down counter Encoder Mode 1 or 2

Question asked by Allen Blaylock on Jun 19, 2018
Latest reply on Jul 3, 2018 by Allen Blaylock
I am trying to configure the TIM2 to act as an up/down counter as describe in Encoder mode 1 or 2. I have the circuit set up to connect PB8 to a count signal and PB9 as a direction signal. I have am having an issue where randomly after an NVIC_Reset the count direction is different dispite the value on PB9 being the same. The itnitialization code is below:
void initializeStepDir()
    TIM_HandleTypeDef timer;
    TIM_Encoder_InitTypeDef encoder;
    // Enable syscfg clock
    // Reset the TIM2 block
    // Enable the TIM2 block

    timer.Instance = TIM2;
    timer.Init.Period = 0xffffffff;
    timer.Init.Prescaler = 1;
    timer.Init.ClockDivision = TIM_CLOCKDIVISION_DIV1;
    timer.Init.CounterMode = TIM_COUNTERMODE_UP;

    constexpr uint32_t FILTER_NUMBER = 3;
    encoder.EncoderMode = TIM_ENCODERMODE_TI1;
    encoder.IC1Filter = FILTER_NUMBER;
    encoder.IC1Polarity = TIM_INPUTCHANNELPOLARITY_RISING; //step signal
    encoder.IC1Prescaler = TIM_ICPSC_DIV1;
    encoder.IC1Selection = TIM_ICSELECTION_DIRECTTI;

    encoder.IC2Filter = FILTER_NUMBER;
    encoder.IC2Polarity = TIM_INPUTCHANNELPOLARITY_BOTHEDGE; //check direction
    encoder.IC2Prescaler = TIM_ICPSC_DIV1;
    encoder.IC2Selection = TIM_ICSELECTION_INDIRECTTI;

    HAL_TIM_Encoder_Init(&timer, &encoder);
    HAL_TIM_Encoder_Start(&timer, TIM_CHANNEL_ALL);
    // NOTE: TI1 -> PB8 TI2 -> PB9



What could cause the system to behave differently given the same inputs? Is this the correct configuration? The stack overflow link in the code suggests that it is for some configuration.