The data that are telemetered from the Fermi spacecraft are not in a form that most users can use for astrophysical analysis. The telemetry is compact and difficult to parse. The instrument teams will process the data that is output from their instruments, producing lists of detected photons with the best estimates of the photons' characteristics. For the LAT, this entails starting with the signals from different components of the LAT resulting from interactions of charged particles, reconstructing the paths of the electron-positron pair produced when a gamma ray interacts with a tungsten atom in the LAT, and then calculating the gamma ray's arrival time, incident energy, and origin. The GBM processing assigns an average photon energy to the detector channels.
Therefore, processing by the instrument teams results in data that are ready for astrophysical analysis stored in a format that the software can read and that is easy to probe. The data from each instrument are described in greater detail elsewhere, but here we discuss the format. The data are stored as FITS files.
Almost all the files that are input to, or output from, the Fermitools are FITS files. FITS stands for 'Flexible Image Transport System,' and the format was originally developed to provide a standard image file format, but has been expanded to provide standards for many different file types used in astronomy. The Fermitools were developed to insulate the average user from the details of the file formats, but as always, additional knowledge can greatly augment your control over the analysis. The general FITS documentation online is extensive, but hopefully this overview will guide you in using this documentation.
FITS files consist of a series of one or more 'Header and Data Units' (HDUs), each of which contains an ASCII header followed by a binary table. The ASCII header describes the contents of the binary table (e.g., the column names and units), and thus the FITS files are largely self-defining. Headers have rows of text consisting of 8 character keywords followed first by the value of the keyword and then by a comment describing the keyword. The first ('primary') HDU is reserved for images, and often has no binary table and only a simple header (called the primary header) identifying the file (e.g., name, date of creation, mission). Subsequent HDUs are called 'extensions.' The de facto standard is that the header for an extension contains copious information pertaining to that extension.
There are standard FITS file formats, for example 'PHA' for a binned spectrum. These standard file formats have required extensions, and required keywords in the headers of these extensions. Similarly, there are standard extensions (with standard keywords) such as EBOUNDS for storing an energy grid that can be used in mission-specific file formats.
A number of tools exist to examine and manipulate FITS files. While we are attempting to create a system that does not require users to master a large number of additional tools, these FITS utilities will give you additional control over your analysis environment. The basic use of these tools is simple to learn. The FTOOLS have a series of tools fcopy, fdump, fmodhead, fplot, and fverify that allow you to examine, copy and manipulate FITS files. The tool 'fv' is a powerful GUI-based utility that should satisfy most needs to examine and modify FITS files. 'fv' will display images, but 'ds9' was designed specifically to display and manipulate images.
The Fermi FITS files were defined to comply with existing standards, particularly those of the Office of General Investigator Programs (OGIP). The OGIP houses the FSSC, similar organizations for RXTE, Swift, Suzaku, INTEGRAL, and XMM, and the HEASARC. Thus conformity with OGIP FITS file standards facilitates multi-mission tools, at least for high energy astrophysics, and assists scientists in analyzing data from different missions.