USGS Spectroscopy Lab

Software

http://speclab.cr.usgs.gov

The Spectroscopy Lab has developed a number of software tools and packages that are of general and specific use in remote-sensing imaging and spectroscopic analysis.

Specpr, Radtran

SPECtral Processing Routines. Spectral analysis system. Radtran is radiative transfer mineral mixture reflectance computations. (Updated 5/2012)

Clark, R. N., 1980, A large scale interactive one dimensional array processing system: Publications of the Astronomical Society of the Pacific, 92, p. 221-224.

Clark, R.N., 1993, SPECtrum Processing Routines User's Manual Version 3 (program SPECPR), U.S. Geological Survey, Open File Report 93-595, 210 pages. http://speclab.cr.usgs.gov/specpr.manual/

Source code can be obtained at: ftp://ftpext.cr.usgs.gov/pub/cr/co/denver/speclab/pub/specpr

Tetracorder information, papers, and source code.

Tetracorder is our mapping software that analyzes spectra and determines what materials are present. (Updated 1/10/2003)

Clark, R.N., Swayze, G.A., Livo, K.E., Kokaly, R.F., Sutley, S.J., Dalton, J.B., McDougal, R.R., and Gent, C.A., 2003, Imaging spectroscopy: Earth and planetary remote sensing with the USGS Tetracorder and expert systems, Journal of Geophysical Research, Vol. 108(E12), 5131, doi:10.1029/2002JE001847, p. 5-1 to 5-44, December, 2003. http://speclab.cr.usgs.gov/PAPERS/tetracorder

Enhancements made after the above 2003 paper are described here:

Clark, R.N., Swayze, G.A., Leifer, I. Livo, K.E., Kokaly, R., Hoefen, T., Lundeen, S., Eastwood, M., Green, R.O., Pearson, N., Sarture, C., McCubbin, I., Roberts, D., Bradley, E., Steele, D., Ryan, T., Dominguez, R., and the Air borne Visible/Infrared Imaging Spectrometer (AVIRIS) Team, 2010, A method for quantitative mapping of thick oil spills using imaging spectroscopy: U.S. Geological Survey Open-File Report 20101167, 51 p. http://pubs.usgs.gov/of/2010/1167/

Full Tetracorder source code can be obtained at: ftp://ftpext.cr.usgs.gov/pub/cr/co/denver/speclab/pub/tetracorder

PRISM and MICA:

Processing Routines in IDL for Spectroscopic Measurements (PRISM) software.
Kokaly, R.F., 2011, PRISM: Processing routines in IDL for spectroscopic measurements (installation manual and user's guide, version 1.0): U.S. Geological Survey Open-File Report 2011b1155, 432 p., available at http://pubs.usgs.gov/of/2011/1155/.

PRISM is a software system for spectroscopic analysis using a graphical user interface (GUI). The software is written in IDL (Interactive Data Language) as a plug-in for computers with ENVI licenses. The modules of PRISM include MICA (Material Identification and Characterization Algorithm), which uses the Clark et al., (2003) Tetracorder spectral feature matching algorithm and allows materials to be identified based on spectral feature comparisons, as well as, material mapping when applied to imaging spectrometer data. PRISM and MICA have functions similar to SPECPR and Tetracorder; however, these systems also have unique capabilities. A comparison of Tetracorder and MICA capabilities is below.

Tetracorder versus MICA


Feature                 Tetracorder        MICA           Notes / Original References
-------------------------------------------------------------------------------------
Runs on Linux              yes              yes
Runs on Unix               yes              yes, Sun Solaris 10
Runs on Windows            yes              yes
Runs on Mac OSX            yes              yes

Interface                command line       GUI
                       (one line start
                          command)

Code                     compiled           IDL
                         C, Fortran,       (compiled)
                         and Ratfor

Source code available      yes              no

Speed: AVIRIS pixels per
  1000 spectral features   3204             140          Speed ratio (Tetracorder/MICA) = 22.8
  per second on Intel     (97% cpu)                      Real time classic AVIRIS ~8000 pixels/second
  Xeon X7542 CPU 2.67GHz                                 Real time NextGen AVIRIS up to ~60,000 pixels/second
  using one CPU, Linux

Expert System            command file     command file   Tetracorder: Clark and others (2003)
                         (ascii)          (ascii)        MICA: Kokaly (2010) different syntax than Tetracorder

Input image format      vicar or ENVI     Any ENVI readable format

Input image organization vicar: BIL       BIL, BIP, or BSQ
                         ENVI: BIL, BIP

Input image data type   vicar: 16-bit int   Any ENVI readable data type
                        ENVI: 16-bit int or
                        32-bit int or
                        32-bit float
                         
Analyze image cube         yes              yes
Analyze single spectrum    yes              yes

Feature Fit Algorithm      yes              yes        Clark and others (2003) algorithm
                                                       Tetracorder: linear correlation coefficient, r
                                                       MICA: user selectable r squared or r

Normalized Red Edge        yes              no         Clark and others (2003)
   Algrithm

Normalized Blue Edge       yes              no         Clark and others (2003)
   Algrithm

Multiple spectral          yes              yes        Clark and others (2003)
  features per material

Multiple Cases per         yes              no         Clark and others (2003)
   material

groups                     yes              no         Clark and others (2003)
group0 (apply to all grps) yes              no         Clark and others (2003)
cases                      yes              no         Clark and others (2003)
pre-ratios                 yes              no         Clark and others (2003)
Feature weighting          auto         user selected  Clark and others (2003)
multiple libraries         yes              yes        Clark and others (2003)
delete bad channels        yes              yes        Clark and others (2003)
Fuzzy Logic (FL)           yes 4.x+         no         Clark and others (2010)

8-bit output               yes              no         Clark and others (2003)
16-bit output              yes              yes        Clark and others (2003)
Weighted FIT output        yes              yes        Clark and others (2003)
Weighted DEPTH outout      yes              yes        Clark and others (2003)
Weighted FIT*DEPTH output  yes              yes        Clark and others (2003)

Output map of unmatched
           pixels        post process       yes
Output summary map       post process       yes
Output image format  vicar with ENVI header vicar with ENVI header
Output preserves
         map/geo info      yes              yes
                       (post process)

Output results viewed      yes              ?
  with any image viewer (post process)

Feature type               auto         user selected  Clark and others (2003)

Diagnostic Features        yes              yes        Clark and others (2003)
Optional Features          yes              no         Clark and others (2003)
Weak features              yes              yes        (set weight =0 in MICA to make a weak feature)
Not features               yes              yes        Clark and others (2003)
Left & right continuaa     yes              yes        Clark and others (2003)
       interval

Continuum Thresholds:
   Left  min, max          yes              yes        Clark and others (2003)
   Right min, max          yes              yes        Clark and others (2003)
  Center min, max          yes              yes        Clark and others (2003)

   Left  min, max w/FL     yes              no         Clark and others (2010)
   Right min, max w/FL     yes              no         Clark and others (2010)
  Center min, max w/FL     yes              no         Clark and others (2010)

 left/right ratio          yes              yes        Clark and others (2003)
 right/left ratio          yes              yes        Clark and others (2003)

 left/right ratio w/FL     yes              no         Clark and others (2010)
 right/left ratio w/FL     yes              no         Clark and others (2010)

Shoulderness:
   Left shoulderness w/FL  yes 4.x+         no         Clark and others (2010)
  Right shoulderness w/FL  yes 4.x+         no         Clark and others (2010)

Feature type:
  Absorption (neg)         yes              yes        Clark and others (2003)
  Emission (pos)           yes              yes        Clark and others (2003)
  Override pos/neg         no               yes        Kokaly (2011)

Other constraints:
  Reflectance * 
    band depth on
    individual features    yes              no         Clark and others (2010)
    

  Individual feature 
    fit constraint      on single           yes     [MICA allows user to set thresholds on individual
                        feature materials             feature fits as well as the weighted sum of fits]
  Individual feature
    depth constraint    on single           yes     [MICA allows user to set thresholds on individual
                        feature materials             feature fits as well as the weighted sum of depths]

  Individual feature F*D
    constraint          on single           yes     [MICA allows user to set thresholds on individual
                        feature materials             feature fits as well as the weighted sum of F*D]


Weighted decision thresholds:
    FIT min                yes              yes        Clark and others (2003)
    FIT min w/FL           yes 4.x+         no         Clark and others (2010)
    DEPTH min              yes              yes        Clark and others (2003)
    DEPTH min w/FL         yes 4.x+         no         Clark and others (2010)
    DEPTH max              no               yes        Kokaly (2011)
    FIT*DEPTH min          yes              yes        Clark and others (2003)
    FIT*DEPTH min w/FL     yes 4.x+         no         Clark and others (2010)
    FITALL min             yes              yes        Clark and others (2003)
    FITALL min w/FL        yes 4.x+         no         Clark and others (2010)
    DEPTHALL min           yes              no         Clark and others (2003)
    DEPTHALL min w/FL      yes 4.x+         no         Clark and others (2010)
    FDALL min              yes              no         Clark and others (2003)
    FDALL min w/FL         yes 4.x+         no         Clark and others (2010)

Additional capability:

   Cluster analysis        yes                         Clark and others (2003)

   Auto-stretched
    jpegs and gifs
    far rapid assessment   yes
    in any image viewer

-------------------------------------------------------------------------------------

References:

Kokaly, R.F., 2011, PRISM: Processing routines in IDL for spectroscopic measurements (installation manual and user's guide, version 1.0): U.S. Geological Survey Open-File Report 2011b1155, 432 p.

Davinci

A tool for 3-D data set manipulations, with intelligence for analyzing imaging spectroscopy data. See http://davinci.asu.edu/ for the latest code.

PicWorks (pw)

PicWorks (pw) Image display, cube spectral extraction, and multiple image overlay package. Pw works on standard X-windows, and has an excellent point and click user interface. It has the most flexible and interactive image stretching we've seen. We use it to create the materials maps shown on this site. Anonymous ftp from ftp://ftpext.cr.usgs.gov/pub/cr/co/denver/speclab/pub/pw

Older Legacy Software

P3

A tool to format 24-bit ppm images for output on the HP Paintjet-300xl and the Designjet-650C, 750C. P3 creates HP RTL output, so it will work with any HP RTL compatible printer. Anonymous ftp from ftp://ftpext.cr.usgs.gov/pub/cr/co/denver/speclab/pub/p3

spview

MS-DOS spectral library database viewer. Anonymous ftp from ftp://ftpext.cr.usgs.gov/pub/cr/co/denver/speclab/pub/spview

Remapp

a simple image processing systems for PC's and Unix systems.
Anonymous ftp pcremapp from ftp://ftpext.cr.usgs.gov/pub/cr/co/denver/speclab/pub/pcremapp
Anonymous ftp remapp for Unix from ftp://ftpext.cr.usgs.gov/pub/cr/co/denver/speclab/pub/remapp.sparc (this is specifically a Sun Sparc version, but should work with most systems with little change.

AVIRIS Geometric Correction Software

U.S. Geological Survey, a bureau of the U.S. Department of the Interior
This page URL= http://speclab.cr.usgs.gov/software.html
This page is maintained by: Dr. Roger N. Clark rclark@usgs.gov
Last modified June 27, 2012.