The Sun, like every main sequence star, due to gravitational collapse, has a small, very hot core in which the temperature is high enough for nuclear fusion to occur. One of the products of the core's inherent incandescence (see Draper's law) is an emitted continuous spectrum of visible light which compiles to the Planck spectrum of "black body radiation". An object that absorbs all radiation falling on it, at all wavelengths, is called a black body. When a black body is at a uniform temperature, its emission has a characteristic frequency distribution that depends on the temperature.
The Sun is approximately 5500K at its photosphere and emits 80% of its energy in the green/yellow range of the visible light spectrum (figure 1A).
The Sun, just like the nebula that formed it, is mostly Hydrogen (74%) and Helium (25%) but it also contains trace amounts of almost every naturally occurring element from Lithium to Uranium (figure 1B).
As the Sun's core releases its continuous spectrum of energy, it is absorbed and re-emitted by the atoms in its many layers. This absorption and re-emission complies with Kirchoff's law in that many absorption lines are created as electrons move to higher energy levels in their respective atoms (figure 1C).
The Sun's outer layers, especially the chromosphere acts as both a relatively cool gas and a hot emission source simultaneously, so as prescribed in Kirchoff's laws, you can observe an absorption line and a re-emission line for the same atoms at the same wavelengths. This allows astronomers to zero in on specific emission lines from the Sun's chromosphere that clearly outline some of the magnetic ferocity occurring on its photosphere and in its chromosphere (figure 1D).
Figure 1: A) Distribution of light emitted by bodies of various temperatures. B) Composition of elements found in the Sun. C&D) Light from a continuous source is absorbed by certain elements at a particular wavelength of light to produce absorption lines in the spectrum. Light can also be emitted by these elements to give rise to emission lines. E) Fraunhofer lines of the solar spectrum.
The Hydrogen alpha re-emission line that astronomers observe in their Hydrogen alpha telescopes, which have become very popular of late, is observed by using a telescope with very precise filters, known as "etalons", incorporated into their optical trains. These filters can block almost the entire visible light spectrum and beyond, while allowing through only the slightest width of visible light present inside the Hydrogen alpha absorption line generated by the re-emission of that same energy from the Hydrogen atom as the electron falls back down to the 2nd energy level. The Sun's outer layers absorb all of the light at that wavelength creating a relatively thick absorption line to the spectroscopic observer, but the re-emission is in every direction away from the atom so only a small portion of it is seen as an emission line by the same observer on Earth.
In the case of the Calcium K telescopes, also very popular now, these scopes use very similar etalons to very precisely examine only a 2-3nm wide bandpass centred on the wavelength emitted as the Calcium atoms re-emit the light absorbed at 393.4nm. The Calcium atoms also shed an electron from their outer shell in this process and become ionized. Hence the formal name Calcium II K line emission.
The various features seen in these Calcium K or H-Alpha telescopes, and in other wavelengths, are clouds of atoms being manipulated by magnetic field lines emanating from the Sun's core. A solar prominence, for instance, is a cloud of atoms that are following along a specific magnetic field line or groups of hundreds of them interacting.
Absorption lines in the Sun's visible light spectrum are shown in figure 1E.
These lines are often segregated into different groups and expressed as the "Balmer series", the "Paschen series” , the "Lyman series" or "Fraunhofer lines" according to the context used (figure 2 A-C).
Figure 2: A-C) Electron orbital movement involved in creating the ‘Fraunhofer’ absorption lines in the Balmer, Paschen and Lyman series.
For a more in depth study of these lines and their emission heights in the solar atmosphere please read Part 1 Spectral line height in the solar atmosphere http://solarnutcase.livejournal.com/9556.html and Part 2 Understanding the bandwidth of your hydrogen alpha filter http://solarnutcase.livejournal.com/9896.html