Spatial regions of interest

The optical density is obtained from absorption spectra using $\mbox{OD}=-\log(I/I_{0})$. With a stack, you must define what pixels consitute an $I_{0}$ region (a blank area in the image), and what pixels make up the $I$ region (the feature you want the spectrum for). In most cases, the easiest way to determine the $I_{0}$ spectrum is to use the Select I0 from histogram button (see Fig. 4). Alternatively, you can specify single pixels with the Add I pixel and Add I0 pixel buttons. If you want to specify a larger region, you are best off using the Add I region and/or Add I0 region buttons, in which case the window shown in Fig. 5 pops up. Control is then temporarily passed to the IDL defroi routine to allow you to define the region of interest. You can now define a region bounded by a polygon by clicking with the left mouse button to define points. Alternatively, you can define a more arbitrary shaped region by holding the left mouse button down and dragging to define the region boundaries. In both cases, you click with the right mouse button to indicate that you've finished making the region. You are then asked to either Accept the region if you like what you did, or to Reject the region if you don't like how it came out. For more details on the behavior of defroi, refer to the IDL manuals. Note that you can add additional regions which may or may not overlap with previously defined regions; if there is any overlap, each pixel is counted only once. The total areas of all $I$ and $I_{0}$ regions are calculated separately, and they are shown to you on the main stack_analyze screen. Finally, you can write regions of interest to a file and read them back as .roi files, as described in Sec. 2.3.

Figure 4: From a histogram of image intensities (top), one can easily define the $I_{0}$ regions (bottom) as being the regions with the highest flux (shown here in red).

Figure 5: Region of interest widget.