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https://github.com/azvoleff/teamlucc

Analysis of land use and cover change using satellite imagery
https://github.com/azvoleff/teamlucc

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Analysis of land use and cover change using satellite imagery

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README 

        
# teamlucc



[![Build Status](https://travis-ci.org/azvoleff/teamlucc.png)](https://travis-ci.org/azvoleff/teamlucc)



## Overview



The `teamlucc` package is designed to facilitate analysis of land use and cover 

change (LUCC) around the monitoring sites of the Tropical Ecology Assessment 

and Monitoring (TEAM) Network. The [TEAM Network](http://www.teamnetwork.org/) 

is a global network of sites in tropical forests wth standardized real-time 

data collection designed to measure tropical forest responses to climate 

variability and change, land cover and land use change, and other threats.



`teamlucc` assists with processing and analysis of remote sensing imagery. 

`teamlucc` supports a range of preprocessing steps and analyses, including: 



* Image selection from USGS archive

    * Parsing metadata files from USGS EarthExplorer

    * Plotting available imagery for an area of interest (AOI), including 

      AOIs that cover more than one path/row

    * Formatting an image order for upload to ESPA system

    * ~~Downloading images from a USGS ESPA order~~ Not working as of 7/1/2014 

      due to changes in the ESPA system.



* Preprocessing

    * Extraction and file conversion of surface reflectance imagery from the 

      Landsat Climate Data Record (CDR) archive

    * Topographic correction using parallel processing (Goslee, 2011)

    * Cloud fill and gap fill (for SLC-off Landsat 7 scenes), including support 

      for the modified Neighborhood Similar Pixel Interpolator (NSPI) and 

      Geostatistical Neighborhood Similar Pixel Interpolator (GNSPI) by Zhu et 

      al.  (2012a, 2012b)

    * Image normalization

    

* Calculation of vegetation indices and image texture measures from grey-level 

  co-occurrence matrices (GLCMs)



* Image classification using random forests or support vector machines



* Change detection using the Change Vector Analysis in Posterior Probability 

  Space (CVAPS) and Double Window Flexible Pace Search (DFPS) algorithms (Chen 

  et al. 2011)



* Accuracy assessment using user's, producer's and overall accuracies, in 

  addition to quantity agreement and disagreement (Pontius and Millones, 2011)



The toolkit is under active development. Follow the [TEAM 

website](http://www.teamnetwork.org/) for news, and the [toolkit project page

on github](https://github.com/azvoleff/teamlucc) for the latest updates.



## Package installation



### Installing `teamlucc`



**NOTE: If you are installing on Windows, you will need to install the 

appropriate version of [Rtools](http://cran.r-project.org/bin/windows/Rtools/) 

for your version of R (as `teamlucc` contains C++ code) before you follow the 

below steps.**



As `teamlucc` is still under development, it is not yet listed on 

[CRAN](http://cran.r-project.org).  The easiest way to install the `teamlucc` 

package is using the 

[`devtools`](http://cran.r-project.org/web/packages/devtools/index.html) 

package by Hadley Wickham.



To install `devtools` type:



```R

install.packages('devtools')

```



at the R command prompt. This will fetch the latest version of `devtools` from 

CRAN. After installing `devtools` type:



```R

library(devtools)

install_github('azvoleff/teamlucc')

```



at the R prompt to install the latest version of `teamlucc`. Typing the above 

command will also work if you already have `teamlucc` installed and want to 

install an updated version of the package.



### Install GDAL



`teamlucc` uses the `gdalUtils` package to facilitate fast image reprojection 

and mosaicking. `gdalUtils` requires having a local GDAL installation. Follow 

the below steps to install GDAL on your system:



#### Windows:



Download the [32bit](http://download.osgeo.org/osgeo4w/osgeo4w-setup-x86.exe) 

or [

64bit](http://download.osgeo.org/osgeo4w/osgeo4w-setup-x86_64.exe) [OSGeo4W](http://trac.osgeo.org/osgeo4w/) installer.



Run the installer. Choose the "Express Desktop Install".  On the "Select 

Packages" screen, ensure the GDAL screen package is checked. You can uncheck 

the boxes for QGIS and GRASS GIS if you don't want them installed (though I 

highly recommend QGIS).



[Edit your environment variables](http://support.microsoft.com/kb/310519):



1. Add "C:\OSGeo4W\bin" (or "C:\OSGeo4W64\bin" if you installed the 64bit 

version) to the "PATH" environment variable.

2. Add a new "GDAL_DATA" environment variable equal to "C:\OSGeo4W\share\gdal" 

(or "C:\OSGeo4W64\share\gdal" for the 64bit version).



#### Linux (ubuntu):



At a shell prompt, type:



``` sh

sudo apt-get install gdal-bin libgdal-dev

```



### (optional) Install IDL and ENVI

[IDL](http://www.exelisvis.com/ProductsServices/IDL.aspx) and 

[ENVI](http://www.exelisvis.com/ProductsServices/ENVIProducts/ENVI.aspx) are

required for running the CLOUD_REMOVE and CLOUD_REMOVE_FAST cloud fill 

algorithms in `teamlucc` (there are also two native R cloud fill routines that 

can be used without an IDL license). IDL and ENVI are also needed to run the 

Landsat 7 SLC-off gap fill routine.



## Using teamlucc



For more information on using `teamlucc`, see the online help in R, and the 

[`teamlucc` webpage](http://www.azvoleff.com/teamlucc). The webpage includes 

examples of a number of specific applications of `teamlucc`, including:



* [Filtering and downloading Landsat 

  scenes](http://www.azvoleff.com/articles/filtering-landsat-with-teamlucc)



* [Preprocessing imagery and 

  DEMS](http://www.azvoleff.com/articles/preprocessing-imagery-with-teamlucc)



* [Cloud removal](http://www.azvoleff.com/articles/cloud-removal-with-teamlucc)



* [Image 

  classification](http://www.azvoleff.com/articles/image-classification-with-teamlucc)



## Installing `teamlucc` Development Version



If you want the very latest version of `teamlucc`, you can install the 

development version. Be aware this version might not install as it is not as 

well tested as the stable version. To install from the `teamlucc` development 

branch, run:



```R

library(devtools)

install_github('azvoleff/teamlucc', ref="development")

```



## Author Contact Information



[Alex Zvoleff](mailto:[email protected])  

Postdoctoral Associate  

Tropical Ecology Assessment and Monitoring (TEAM) Network  

Conservation International  

2011 Crystal Dr. Suite 500  

Arlington, VA 22202  

USA



## References

Chen, J., Chen, X., Cui, X., Chen, J., 2011. Change vector analysis in 

posterior probability space: a new method for land cover change detection. IEEE 

Geoscience and Remote Sensing Letters 8, 317--321.



Goslee, S.C., 2011. Analyzing remote sensing data in R: the landsat package. 

Journal of Statistical Software 43, 1--25.



Pontius, R.G., Millones, M., 2011. Death to Kappa: birth of quantity 

disagreement and allocation disagreement for accuracy assessment. International 

Journal of Remote Sensing 32, 4407--4429.



Zhu, X., Gao, F., Liu, D., Chen, J., 2012a. A modified neighborhood similar 

pixel interpolator approach for removing thick clouds in Landsat images. 

Geoscience and Remote Sensing Letters, IEEE 9, 521--525.



Zhu, X., Liu, D., Chen, J., 2012b. A new geostatistical approach for filling 

gaps in Landsat ETM+ SLC-off images. Remote Sensing of Environment 124, 49--60.