The stack_analyze File drop-down menu

The stack_analyze File menu is shown in Fig. 2. The stack input/output options in this menu are:

Build stack list ``.sl'' file calls stack_buildlist (see Sec. 2.5 and Fig. 10) to build a list of the image files that are in the stack.

Read stack list ``.sl'' file reads in a sequence of images from a stack list file (see Fig. 8). All regions of interest and alignment shifts are wiped clean.

Figure 8: Reading a stack list .sl file.

Write stack list ``.sl'' file writes the list of files of this stack, and their alignment, out to a file.

Read stack ``.stk'' file reads in a binary stack file. All regions of interest and alignment shifts are wiped clean.

Read aXis stack ``.ncb'' file reads in a binary stack as written from Adam Hitchcock's aXis program. Note that these files store data as integers with a scaling factor, so there is the potential for a slight loss of precision in the data. Also, the .ncb file must be accompanied by its matching .dat file. The .ncb file is a binary file with little endian byte order; stack_analyze should read and write these without a problem on both little endian (e.g., Intel) and big endian (e.g., PowerPC) computers.

Read I0 csv (ev,khz) file reads in an $I_{0}$ file, in case you have it in a separate measurement. This is described further in Sec. 2.8.

The next set of options concern .stk files; the format of these files is described in Sec. B.

Save stack ``.stk'' file saves the stack as it now exists (and is now aligned) to a binary stack file.

Clip to square and save ``.stk'' file lets you drag a box over the image and select only a spatial subregion for further analysis. This subregion will be saved to a file.

Clip to I region and save ``.stk'' file is illustrated in Fig. 9.

Write aXis stack ``.ncb'' file writes out a binary stack which can be read by Adam Hitchcock's aXis program. Note that these stacks have the data stored as integers with a scaling factor, so there can be a slight loss of precision when data is stored in this format. This routine will also write out the .dat file that accompanies the .ncb file. The .ncb file is a binary file with little endian byte order; stack_analyze should read and write these without a problem on both little endian (e.g., Intel) and big endian (e.g., PowerPC) computers.

Figure 9: You can clip a stack to show only the $I$ region. To do this, you must first define one or more $I$ regions, and one or more $I_{0}$ regions (left). The areas outside the $I$ region are then filled with the $I_{0}$ spectrum and the overall image field is trimmed down to just barely contain the $I$ region (right).

        

Save autoclipped ``.stk'' file saves a binary stack file of only the pixels that are present in every single image in the stack. That is, as images have been shifted around in alignment, there may be some features that appear at the edges of some images but fall outside the field of view of other images. These edges which are not present in all of the files are clipped out and the file is saved. It is generally recommended that you save an autoclipped stack, and use it for your subsequent work, after you're happy with the stack's alignment!

The alignment items in the menu are:

Apply ``.aln'' alignment file applies an independently-determined set of $X,Y$ shifts (in pixels) to a stack. You should not normally need to use this option.

Align stack invokes the stack_align routine to align a stack, as described in Sec. 2.6.1.

Manually align stack invokes the manual alignment routine stack_manalign as described in Sec. 2.6.2. Hopefully you won't have to use this too often.

Save ``.aln'' alignment file lets you save the alignment information only to a comma space value file. Since this information is also saved in the stack list .sl files, you should not normally need to use this option.

Note that when you've finished the alignment, you'll probably want to save an updated version of the stack list, and save an autoclipped version of the stack as well.

The processing options are:

Despike stack

When using a gas-filled proportional counter, sometimes you can get single pixels with very large values (one or a few bright white dots) due to electrical discharges, cosmic rays hitting the detector, and so on. This option looks for such pixels and sets them to the average of their neighboring pixels for all images in the stack.

Noise filter

is meant for filtering out periodic frequencies. It may be useful for getting rid of non-random line noise for example. See Sec. 2.7 for more info.

The next choices involve saving results of your work:

Save all but movie, data saves a region ``.roi'', a spectrum ``.xas'', a png spectrum ``s.png'', and an image ``.png'' file, all with the same filename header.

Save spatial region ``.roi'' lets you save your regions of interest (see Sec. 2.4.1).

Save spectrum ``.xas'' lets you save the spectrum you see on the screen. The ``.xas'' file format is discussed in Sec. 2.3; such a file can be read in by Excel, for example.

Save PNG spectrum ``s.png'' saves a PNG image of your spectrum.

Save image ``.png'' saves the image you now see as a PNG file.

The items Save movie ``m.gif'', Save movie ``.mpg'', Save movie ``m.gif'' (no spectrum), and Save movie ``.mpg'' (no spectrum), all save movies of the stack with or without the spectra. See Sec. 2.10 for more information.