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Problem with spectral profile of CRISM image within ENVI/CAT software


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I am a student who is very new to working with CRISM and CAT/ENVI software. I am trying to look up the spectral profile of pixels within a CRISM image of the Endeavour crater. The Observation ID of this image is  FRT0000CE1D_07_IF166L_TRR3. The image has been converted to CAT from PDS. As well, a photometric correction (division by cos(i)) was applied to the trr3 image prior to looking up the Z profiles. I have not run any other corrections as is has been mentioned in other forums that trr3s have been cleaned before being available to the public.   henever I bring up the spectral profile for any pixel within the image the x axis values are shown backwards (3.5  - 1.5). As well, the actual profile itself looks like a a sharp spike around the 2.75 micron region but drops down to 0 again.


I have a project I must finish by next week. Please respond asap if you know what steps i am missing!





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Hi Colin,


First, about the big spike at 2.75 microns:


There are bad bands in the CRISM data in that region that are filled with "65535." When autoscaled that obviously drives the y axis way out of range so that you don't even see the actual I/F data, which is all normally < 1.


There are two z-profile menu items available in CAT/ENVI on the display window Tools menu. The one called "Z Profile (Spectrum)" is the native ENVI routine, and it does not recognize the 65535 as a bad value flag (even though it's specified in the header). So that spectral plot ends up dominated by the spike, as you describe. You can fix that as follows. In the Edit menu on the spectral plot, go to "Plot Parameters...", click the "Y-Axis" radio button, and then enter a reasonable value in the second "Range" box (that should start out filled with 65535). You can usually start out with 0.5 or so and adjust from there. Hit "Apply" at the bottom to adjust the plot.


The other Z profile tool is a custom CRISM one called "**CRISM**CDR Z Profile..." and it ignores the 65535 values and does a better scaling on the y axis. However, it does not update as you interactively move around the image like the ENVI profile does. You get a plot for one pixel, and then if you want to see another pixel you have to move there and do another profile.


Second, about the wavelength axis labeling order:

Maybe you're plotting the spectral profile from the wrong display here. You may have multiple display windows open, some showing CAT-converted data, and some showing the original CRISM data which is not swapped. Each window has its own Tools/Z Profile command, which will pull a spectrum from the file that window is displaying. So even if you've done the CAT conversion, if you go to the Tools menu on a display for the raw CRISM data, you get a spectrum with reversed wavelengths. Make sure you use the Tools menu on the display for the CAT-converted data. It should plot wavelengths in the order you want.


One note on that - the spectral plot with reversed wavelengths is not exactly wrong, the spectral data is reversed along with the axis labels; so it's technically accurate, even if it's not what you ultimately want. At least it should be. You can check by looking for a couple of characteristic, ubiquitous features. You should see a narrow "triplet" feature at 2.0 microns when you haven't done a volcano scan correction. And going from shorter to longer wavelengths, the spectrum should dive at about 2.7 and then ramp up between there and 3.7 or so microns. If the axis labels don't match up with those features there is a more serious problem.


And one more general note. You mention not doing any further corrections because the TRR3 data is already cleaned. You probably should run a volcano scan atmospheric correction to remove the CO2 feature at 2 microns, unless you're studying that atmospheric feature. That's not removed in TRR3 TRDR data. But you don't generally need to run the data filtering utilities.




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Thanks for your help Frank. I have resolved the issue to an extent. I can now make sense of the spectral profile for each pixel. However,  I have run the volcano scan like you said (Division by scaled volcano observation - Empirically optimized for this observation) but I seem to still be getting a spike at the 2.7 micron wavelength. Should I try replacing the empirical optimization parameter with a different option in order to reduce this spike?



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I think you'll always get the gigantic spike at ~2.7 microns, and the reason is the same - there are pixels set to 65535 to flag bad bands there, and that flag value is carried through all the processing steps. If you manually rescale the spectral plot it should look OK at other wavelengths.


You may also get smaller spikes (few percent of continuum) in the 1.9-2.1 micron range because of artifacts from the volcano scan correction. The empirical volcano scan optimization is supposed to minimize these artifacts. You might want to experiment with using different volcano scans (you can select your own with the "User-selected volcano scan" option), but this should not have much effect away from the region right around 2.0 microns.

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