08/25/2009

Spectrum Image Example

How to load a spectrum image and plot the sum spectrum.

1.  Open the spectrum image.  Usually, this is done with the File / Open menu in the Lispix Menu Bar.

• This is the Lispix menu bar.  The file menu is on the far left.  Clicking on the file menu gives this:
• Use the OPEN menu for spectral images stored as .raw, .spd or .ser files.  (See What Lispix Reads for more information).
• Select the file.  A progress bar will show the time needed to load the file.  (The loading can be interrupted by closing the progress bar (by clicking on the "X" in the upper right corner of the progress bar.
•   .

• The spectrum image will appear, along with a "slice slider".  Select the image plane for display by moving the slider.
• ------^------ Change slices by dragging this slider.

You can view the spectral image in a variety of ways using the Data Cube Tool.

• Open the Data Cube Tool using the TOOLS Menu in the Menu Bar.
• To see a sum spectrum, use the first menu item in the plot button
• The plot button is circled above.  This is its menu:
• The Sum Spect for whole cube menu will show a progress bar, then the desired plot:

• The Multi spect - whole cube takes more time, and shows four additional plots (derived spectra) which are likely to show features in the data that the Sum Spectrum does not show.  I use this immediately after opening a spectral image to get a quick overview of its contents.
• The multi-spectrum-plot above has been expanded by dragging the bottom edge of the plot downwards.  The buttons across the bottom show or hide the corresponding plot.
• All of these plots have been normalized to 1.0.  You can display them separately in their own plot with the counts in the y-axis, by using their appropriate menu.
• Sum:  sum spectrum for whole cube.  Each point represents an image from a particular channel, or x-ray energy.  The value at any point or channel number, is the sum of the pixel values for that image.
• Max:  analogous to sum, except that the value is the maximum value for the image.
• Log sum:  log of the sum spectrum above.
• Log running sum and running max.  These are analogous to the Log sum and Max plots, except they are taken from a running-sum spectrum image, where each image plane is the running sum of 10 consecutive images.  The peaks are smoothed considerably and broadened a little.
• In order to save memory, the running-sum spectrum image is not saved or displayed.
• To see a running sum cube for any N consecutive images, use Cube / running sum
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