##############   KNOWN ISSUES   ################################################

ALL RESULTS SHOULD BE CHECKED FOR ACCURACY as calibration can throw off
identifications, and check that the Tetracorder expert system adequately
covered the environment.   Either condition (error in calibration to
reflectance, or minerals or other materials in the environment that
are not covered by the expert system used) can cause misidentification.
Thus, spectral features should be extracted from the image cube(s) for
each identified component that is important to your study and checked
that the spectral features in that unit are consistent with known spectral
properties for that material.  Ideally, important identified components
are verified by field work collecting samples when possible.

Please understand the diagnostic nature of absorption features in minerals.
Broad electronic absorptions have a lot of similarities between minerals,
especially Fe2+ bearing minerals.  Therefore many tetracorder output files 
include generic in the file names.  The specific mineral in the name is 
so you know the reference spectrum used, not that that specific mineral
was identified.

A good example of diagnostic nature of absorption features is illustrated
in the organics confusion below.


ISSUES for: cmd.lib.setup.t5.2e1 +

#########################################################################################
###### Spectra of shallow water can mimic broad electronic absorptions, commonly Olivine

Water has multiple absorptions in the near infrared and in shallow
water, the absorptions overlap such that there is a broad decrease in
reflectance from the visible to IR and when the continuum is removed,
mimics the broad absorption like that seen in olivine.  If tetracorder
maps olivine near lake shores or shallow streams, it is likely that this
condition is giving a false positive.


#####################################################################################
###### Organics Confusion

The spectral signatures of organics are similar and telling organics apart
at the typical spectral resolutions of imaging spectrometers is difficult.
While separating aliphatic from aromatic hydrocarbons or organics with
single, double or triple bonded carbons atoms is possible at spectral
resolution typical of imaging spectrometer (e.g. AVIRIS, CRISM, VIMS),
identifying specific organics is not possible.  For example, one AVIRIS
scene mapped clay minerals + gasolene along a portion of a highway.
Was raw gasoline spilled in that area?  No.  Trash, which contains
plastics, are mainly aliphatics hydrocarbon and have absorptions close
to the aliphatic hydrocarbons in gasolene at AVIRIS spectral range
and resolution.  A higher spectral resolution spectrometer and/or
ground checking would be necessary to distinguish the possibilities.
Understanding such limitations of spectroscopy and the Tetracorder
identified results is important.


#####################################################################################
######  High-iron olivine and magnetite absorptions are similar in the near-IR

High-iron olivine and magnetite have broad electronic absorptions that
can appear similar and make it difficult to distinguish between the
two in the near-infrared.  To better aid in separation, more high iron
olivines as a function of grain size and magnetites as a function
of grain size are needed to distinguish between these two minerals.


#####################################################################################
###### Prehnite - Chlorite confused with kaolinite + calcite + dry vegetation mixture

prehnite+.50chlorite can map with a kaolinite + calcite + dry vegetation mixture
           - observed in Arches 1995 Aviris data

this is mitigated to some degree in cmd.lib.setup.t5.2+ series, but not completely.

#####################################################################################
###### Snow detected in some vegetation:

One of the expert system known deficiencies is desert types of vegetation
which have broad water bands that are shifted to longer wavelengths
than typical vegetation, and the closest match is ice and melting snow.
More vegetation spectra need to be added to the expert system.  
Mitigation: if you knew the temperatures were above freezing everywhere in
your data, snow/ice could be rejected.  Thus, if your imaging spectroscopy
data are in warm environments, set the temperature above 0 C.  This can
be difficult if in mountainous terrain.

#####################################################################################
######  Sphalerite

Sphalerite is not a diagnostic detection, only a general shape match so could
be other things.

#####################################################################################
######  Azurite.

If there are Fe2+ absorptions along with a carbonate band, it can be
misidentified as azurite.  Fe2+ bands are very similar over a wide
variety of Fe-bearing minerals, and can be similar to the Cu absorption
in azurite.  Detections of azurite should be field checked if important.

#####################################################################################
######   Epidote

Epidote is usually identified well.  If you see it mapping over broad areas,
it may indicate a calibration error, or another compound is causing confusion.

#####################################################################################
###### Areas where no minerals map

Check the vegetation maps to see if vegetation was thick in the areas
where no minerals mapped.  Tetracorder will try and detect minerals
when the vegetation is sparse enough, but as the vegetation thickens,
it gets more difficult.  If there is little vegetation in the areas where no
minerals mapped, it is likely due to 1) the minerals covered byt the spectrometer
used do not have absorptions in that wavelength region, or 2) the surface is wet.
Water is very absorbing in the near infrared and will suppress photon path
length into the ground, making mineral detection difficult.

#####################################################################################
######  Sericite

Sericite is a fine grains muscovite/illite/paragonite, so check those three minerals. 

#####################################################################################
######  Magnetite

Magnetite is very dark with a broad iron absorption that is not terribly diagnostic
and can be confused with the borad iron absorption in a high iron olivine.
Look in the group.1.5um-broad and results.group.1.5um-broad directories.


#####################################################################################
###### 

