Program by Jonathan Greenberg
Property of the CSTARS Lab at the University of California, Davis. Please ask for permission before distributing this script.

Introduction:

MATLAB function for performing red edge vegetation analyses on hyperspectral datasets using a cubic polynomial interpolation. The function returns the wavelength location of the red edge.

System Requirements:

This program needs quite a bit of memory, but you can modify this somewhat by lowering the "maxPixelRead" value.

• Unix users: make sure you have enough swap space (talk to your sysadmin).
  
• Mac users: you'll want to turn virtual memory WAY up if you do not have sufficient RAM, and then allocate more preferred memory for the application. To do this, SINGLE click on the MATLAB application and hit Command-I ("Get info" if you want to use the File menu). Older OSs will see the "Memory requirements" dialog-- change the "Preferred Size" to a much larger number, depending on your input filesize. Close the MATLAB info window and boot the program. Newer OSs should click where it says "General Information" and change it to "Memory". Follow the above steps for upping the memory. For AVIRIS scenes I typically set this value for 500 or 600 megs. Feel free to complain to Mathworks about their decision to not support a MacOS X version of MATLAB if you get frustrated with dealing with out-of-memory errors.
  
• Windows users: make sure you have enough virtual memory.

With enough memory, this can be fairly speedy, but if it starts using virtual memory it can take awhile. Be patient. Go get some coffee and come back later.

Instructions:

1. Unzip the file with your favorite decompressor-- Unix users use "unzip [filename]", Macintosh users can use Stuffit Expander and Windows users have a myriad of decompressors (usually WinZip is the unzipper of choice).

2. Place the redEdge.m file in your MATLAB:Toolbox:local folder.

3. You will need to first create a list of the wavelengths in BAND order of the sensor. A down-and-dirty way of doing this is to open the header of the image file and copy and paste the wavelengths into a separate text file. Each wavelength should be on a separate line. We used a text editor to search and replace all the commas with returns. Remember that it is important that you do NOT sort the wavelengths-- sensors like AVIRIS record data somewhat out of order, but we account for this in the program and you will get errors if you try to sort it.

Note: We have included several inWaveFiles:

• AVIRISwave.txt: AVIRIS bands
• HYMAPwave.txt: HYMAP bands
• ASDFRwave.txt: ASD FR Spectrometer bands.

4. The command to initiate the function is "feval('redEdge',inBipFile,byteOrder,dataType,inWaveFile,numPixels,header,minWave,maxWave,maxPixelRead,outBipFile)".

• inBipFile: the filename of the image to analyze in BIP format.
• byteOrder = this is the numerical format of the input file following ENVI header standards with a modification to include text files. The following lists the codes:
  • 0 = Least Significant Byte First (DEC and MS-DOS)
  • 1 = Most Significant Byte First (SUN,SGI,IBM,HP,DG)
  • 99 = CSV (columns = samples, rows = bands)
• dataType: this follows the ENVI header style, where:
  • 1 = 8-bit byte
  • 2 = 16-bit signed integer
  • 3 = 32-bit signed long integer
• inWaveFile: the unsorted list of wavelengths from the sensor (see step #3).
  
• numPixels: the number of pixels or samples in your input file. For images, this is the number of samples x the number of lines.
  
• header: the header offset-- usually just 0. Once again... check the header.
  
• minWave and maxWave: minimum and maximum shoulders of the red edge -- determine by looking at the data first, choose regions that contain a less noisy red edge for best results. I have found that AVIRIS and HYMAP datasets usually have a fairly clear red edge region.
  
• maxPixelRead: this was implemented as a memory management function to avoid entering virtual memory by processing the data in chunks and appending the output to a file instead of trying to load the entire image into memory and then attempting to process it. Try a value around 2000. This is the maximum number of pixels read into memory at a time.This currently does not matter if you are using 'text' as your file format.
  
• outBipFile: the continuum removal output-- it will be the same number of samples and lines in BIP format, 1 band, header offset = 0 and the data type is double precision. If you choose 'text' as your input file type, the output file will be a CSV file of 1 row and numPixels columns.

Change Log:

2.4

• Removed the inBipFileFormat argument and replaced it with improved byte order and data type support.
• Attempted to use ENVI standard header arguments.

2.2:

• Removed samples and lines input argument and replaced it with numPixels to allow for non-image datasets such as spectrometer outputs.
• Removed the bands argument (it is now automatically determined by the number of bands in the inWaveFile).
• Added inBipFileFormat for better control over numerical formats
• Added the capability of importing CSV files (use inBipFileFormat = 'text' to use this feature).
• Added the inWaveFile for the ASD FR Spectrometer ('ASDFRwave.txt').
• Added the inWaveFile for the HYMAP aerial sensor ('HYMAPwave.txt').
• Renamed the AVIRIS inWaveFile ('AVIRISwave.txt').

2.1: Added "maxpixelread" argument which reduces memory usage significantly.
2.0: Original release of the red edge by interpolation function.

Bugs:

• The inWaveFiles were created on a Macintosh, so it may be neccessary to either convert them or recreate them from the headers if they do not work.
• In ENVI, try using Host(Intel) as the Byte Order when importing the output.

Contact:

Jonathan Greenberg, greenberg@ucdavis.edu.

The software on this page has been created by CSTARS members, and may be freely downloaded by outside users. However, if you wish to distribute or use the source code of these applications, please ask permission from the author(s) first. The author, CSTARS and the University of California take no responsibility for any damage this software may create.