An encoder spectrograph is used to analyze radiation from one or more samples in various configurations. The radiation is analyzed by spatially modulating the radiation after it has been dispersed by wavelength or imaged along a line. Dual encoder spectrographs may be used to encode radiation using a single modulator. An encoded photometric infrared spectroscopy ("EPIR") analyzer employs orthogonal encoded components having substantially identical modulation frequencies, which may allow for the multiplexing of up to twice as many encoded components.