integrate -- Integrate regions of interest on spectra


integrate spectrum area-of-interest


Integrates areas of interest in 1-d and 2-d spectra. spectrum is the name of the spectrum to integrate. area-of-interest is either a gate that can be displayed on the spectrum (due to the set of parameters defined on the gate and the set of parameters the spectrum displays), or a set of points in parameter space that define an integration region.

integrate Integrates a spectrum within some selected area of interest. The command returns the centroid, total number of counts and full width at half maximum under gaussian peak shape assumption.

The spectrum can be any kind of spectrum, although clearly, some spectra have integrations that may not be very meaningful (e.g. summary spectra). The area of interest can either be a gate name or a list of points that describe the area of interest.

If the area of interest is a gate name it must be the name of gate of suitable type that can be displayed on the spectrum. Suitable means that if the spectrum is 1-d the gate must be a slice like gate, while if the spectrum is 2-d the gate must be a contour like gate. Displayable means that if you displayed the spectrum in Xamine, you would see the gate displayed on that spectrum. In general, that means that the parameters that the gate is defined on are the same as the parameters the spectrum is defined on.

If the area of interest is a set of points, for 1-d spectra, the points must be a Tcl list that is a pair that specifies the boundaries of the integration region. The points must be specified in the coordinate system of the parameter the spectrum is defined on, rather than in spectrum channels (note that it is possible, but not necessary, that the spectrum was defined in such a way that these two coordinate systems are the same.

For example; Consider a spectrum defined:

spectrum aSpectrum 1 aParameter {{0 1023 512}}

The command:

integrate aSpectrum [list 200 300]               

Will integrate the spectrum from channels 100 through 150 because the spectrum is specified as a 2:1 compresssion of the parameter to spectrum channels.

If the area of interest is a set of points for a 2-d spectrum, the points must be a list of coordinate pairs (again in parameter coordinates not channels), that define the vertices of a closed polyfigure (line crossings are allowed, and there must be a minimum of three points). The interior of the polygon is defined in the same way the interior of a contour is defined: For any point, extend a ray to infinity in any direction. If the line crosses an odd number of line segments defining the polygon the point is inside otherwise outside.

For example:

integrate a2dSpectrum [list [list 0 0] [list 100 0] [list 100 100] [list 0 100]]

Integrates a square that has one vertex at the origin and has a side 100 parameter units.

The command returns a Tcl list that contains the integration centroid, the number of counts in the region of interest, and the Full width at half maximum (FWHM) under the assumption the region of interest encloses a single peak with a gaussian line shape. If the spectrum is a 2-d spectrum, The centroid and FWHM are returned as pairs that describe the x and y centroids or FWHM's in the X and Y directions respectively.