Terahertz Transmission

The ratio is the measurement. Both scans are transformed and the sample spectrum is divided by the reference, so everything common to the two — the emitter, the detector, the optics, the water lines — cancels. That only holds if nothing else changed between them. A realigned beam or a different purge level shows up as fake structure in the transmission.

Dynamic range is the honest limit. The noise floor is estimated from the quiet stretch before the pulse arrives. Where the reference drops within about 10 dB of that floor, the ratio is noise divided by noise and the transmission there means nothing, however smooth it looks. The usable-bandwidth figure is where that happens.

Windowing is a choice, not a default. Cutting the record before an internal echo removes the Fabry–Pérot ripple, at the cost of frequency resolution. Leaving the echo in keeps resolution and gives you the ripple. The tool does whichever you ask and tells you the resolution you ended up with.

Index and absorption assume a simple slab. With a thickness, the tool uses n = 1 + cΔφ/ωd and takes the Fresnel losses off the amplitude. That is the standard thick-sample extraction and it ignores multiple internal reflections, so it is right when the echo is outside your window and approximate when it is not. Thin or strongly absorbing samples need a proper iterative fit, not this.