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From the energy equation head loss can be expressed as a function of the difference in the pressure, velocity, and height difference.
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$$
h_L = {P_1 - P_2\over {pg}} + {V_1^2 - V_2^2\over {2g}} + {z_1 - z_2}
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Since flow is controlled by the peristalic pump, the flow is constant, and since the tube diameter is also constant, there would be no difference in the velocity.
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If the pressure difference is measured when there is no flow, then the head loss and the velocity terms from the energy equation would be zero. This allows the height difference to be expressed as the pressure reading from the standing water.
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The pressure reading from the standing water is subtracted from the measured pressure difference values to cancel out the height term. The resulting pressure difference corresponds directly to head loss of the rotameter.
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