stack_analyze: the main screen

The stack_analyze routine is the main program used for analyzing stacks. It produces a screen like what is shown in Fig. 1.

Figure 1: The stack_analyze main screen.

Figure 2: The File drop-down menu in the program stack_analyze.

You can choose to display either the transmitted flux or the optical density $\mbox{OD}=-\log(I/I_{0})$. You can adjust the contrast of the image by playing with min, max, and gamma. The image is displayed as

$$\mbox{display}=\left(\frac{\mbox{image}-\mbox{min}} {\mbox{max}-\mbox{min}}\right)^{\mbox{gamma}}.$$ (1)

The program starts out displaying the full range of the data at a contrast of gamma=1. You can adjust the colormap used to display the image with the Colors button, but only on 8 bit graphics devices. To change the image that is shown, click on it in the Image to display list. ``Bad'' images should be removed from the stack; see Fig. 3 for an example. Finally, movie options are discussed more in Sec. 2.10. Finally, at the top of the screen there is an option for Post analysis which includes a call to the IDL slicer3 routine as well as a dose estimation menu (see Sec. 2.9).

Figure 3: To remove a bad file from a stack, select it from the file display list and click on the Remove this image from stack button.