Skip to content

Commit

Permalink
merge fixes from devbr6
Browse files Browse the repository at this point in the history 
git-svn-id: https://svn.osgeo.org/grass/grass/trunk@56706 15284696-431f-4ddb-bdfa-cd5b030d7da7
  • Loading branch information
@HamishB
HamishB committed Jun 15, 2013
1 parent b3d30a7 commit 87a78c8
Showing 1 changed file with 97 additions and 58 deletions.
155 changes: 97 additions & 58 deletions raster/r.li/r.li.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,53 +9,66 @@

<img src="grass_logo.png" alt="GRASS logo"><hr align=center size=6 noshade>


<h2>NAME</h2>

<em><b>r.li</b></em> - Landscape structure analysis package overview.


<h2>KEYWORDS</h2>
raster, landscape structure analysis, landscape metrics, landscape pattern, landscape analysis

raster, landscape structure analysis, landscape metrics,
landscape pattern, landscape analysis


<h2>DESCRIPTION</h2>

The <em>r.li</em> suite is a toolset for multiscale analysis of landscape structure.
It aims at replacing the <em>r.le</em> suite of modules through a client-server,
multiprocess implementation. External software for quantitative measures of landscape
structure is for example FRAGSTATS (McGarigal and Marks 1995).
<p>The <em>r.li</em> suite offers a set of patch and diversity indices.
It supports analysis of landscapes composed of a mosaic of
patches, but, more generally, the modules work with any two-dimensional
raster map whose cell values are integer (e.g., 1, 2) or floating point
(e.g., 1.1, 3.2) values. The <em>r.li.setup</em> module has options for
controlling the shape, size, number, and distribution of sampling
areas used to collect information about the landscape structure.
Sampling area shapes can be the entire map or a moving
window of square, rectangular or with circular shape. The size of
sampling areas can be changed, so that the landscape can be analyzed
at a variety of spatial scales simultaneously. Sampling areas may be
distributed across the landscape in a random, systematic, or
stratified-random manner, or as a moving window.
<p>The <em>r.li</em> modules can calculate a number of measures that produce
single values as output (e.g. mean patch size in the sampling area),
as well as measures that produce a distribution of values as output
(e.g. frequency distribution of patch sizes in the sampling area). The
results are stored as raster maps.

<p>The general procedure to calculate an index from a raster map is two-fold:
The <em>r.li</em> suite is a toolset for multiscale analysis of landscape
structure. It aims at replacing the <em>r.le</em> suite of modules
through a client-server, multiprocess implementation. External software
for quantitative measures of landscape structure is for example FRAGSTATS
(McGarigal and Marks 1995).
<p>
The <em>r.li</em> suite offers a set of patch and diversity indices. It
supports analysis of landscapes composed of a mosaic of patches, but,
more generally, the modules work with any two-dimensional raster map
whose cell values are integer (e.g., 1, 2) or floating point (e.g., 1.1,
3.2) values. The <em>r.li.setup</em> module has options for controlling
the shape, size, number, and distribution of sampling areas used to
collect information about the landscape structure. Sampling area shapes
can be the entire map or a moving window of square, rectangular or with
circular shape. The size of sampling areas can be changed, so that the
landscape can be analyzed at a variety of spatial scales simultaneously.
Sampling areas may be distributed across the landscape in a random,
systematic, or stratified-random manner, or as a moving window.
<p>
The <em>r.li</em> modules can calculate a number of measures that produce
single values as output (e.g. mean patch size in the sampling area), as
well as measures that produce a distribution of values as output (e.g.
frequency distribution of patch sizes in the sampling area). The results
are stored as raster maps.

<p>
The general procedure to calculate an index from a raster map is
two-fold:

<ol>
<li>run <em>r.li.setup</em>: create a configuration file selecting the parts of
raster to analyze.
<li>run <em>r.li.setup</em>: create a configuration file selecting the
parts of raster to analyze.

<li>run <em>r.li.'index'</em> (e.g., <em>r.li.patchdensity</em>) for calculate the selected
index using on the areas selected on configuration file.
<li>run <em>r.li.'index'</em> (e.g., <em>r.li.patchdensity</em>) for
calculate the selected index using on the areas selected on
configuration file.
</ol>

<h2>NOTE</h2>

Also the <em>r.li.daemon</em> has a main function and it can be run, but it is only a
template for development of new indices.
<h2>NOTES</h2>

Also the <em>r.li.daemon</em> has a main function and it can be run, but
it is only a template for development of new indices.
<!-- mhh ??: -->
The function itself has no meaning, it can be used only for debug.
The function itself has no meaning, it can only be used for debugging.


<h2>EXAMPLE</h2>

Expand All @@ -67,40 +80,42 @@ <h2>EXAMPLE</h2>
<ol>
<li> run
<div class="code"><pre>
r.li.setup
r.li.setup
</pre></div>
<li> The main <em>r.li.setup</em> window is displayed, click on "New"
<li> Now it is displayed the new configuration window,
enter the configuration file name (e.g., "my_conf", do not use absolute paths)
and the name of raster map (e.g., "geology").
The other fields are not needed for this configuration.
<li> Now it is displayed the new configuration window, enter the
configuration file name (e.g., "my_conf", do not use absolute
paths) and the name of raster map (e.g., "geology"). The other
fields are not needed for this configuration.
<li> Click on "Setup sampling frame", select "Whole maplayer" and click "OK"
<li> Click on "Setup sampling areas", select "Moving window" and click "OK"
<li> Click on "Use keyboard to enter moving window dimension"
<li> Select "Rectangle" and enter 5 on "heigth" and "width" fields
<li> Click on "Save settings"
<li> Close <em>r.li.setup</em> window
<li> Close the <em>r.li.setup</em> window
</ol>

<li> CALCULATE PATCHDENSITY INDEX
<ol>
<li> set region settings to geology raster map:
<ol>
<li> set the region settings to the "<tt>geology</tt>" raster map:
<div class="code"><pre>
g.region rast=geology -p
g.region rast=geology -p
</pre></div>
<li> run <em>r.li.patchdensity</em>:

<li> run <em>r.li.patchdensity</em>:
<div class="code"><pre>
r.li.patchdensity map=geology conf=my_conf out=patchdens
r.li.patchdensity map=geology conf=my_conf out=patchdens
</pre></div>
</ol>
</ol>

The resulting patch density is stored in "patchdens" raster map.
The resulting patch density is stored in "<tt>patchdens</tt>" raster map.

You can verify the result for example with contour lines:
<div class="code"><pre>
r.contour in=patchdens out=patchdens step=5
d.rast patchdens
d.vect -c patchdens
r.contour in=patchdens out=patchdens step=5
d.rast patchdens
d.vect -c patchdens
</pre></div>

Note that if you want to run another index with the same area
Expand All @@ -112,6 +127,7 @@ <h2>EXAMPLE</h2>
configuration file on a 200x200 raster map, then the sample area is
10x10.


<h2>SEE ALSO</h2>

<b>Core modules</b>:
Expand All @@ -127,26 +143,31 @@ <h2>SEE ALSO</h2>
<li> <a href="r.li.patchdensity.html">r.li.patchdensity</a>: Calculates patch density index on a raster map, using a 4 neighbour algorithm</li>
<li> <a href="r.li.patchnum.html">r.li.patchnum</a>: Calculates patch number index on a raster map, using a 4 neighbour algorithm</li>
</ul>

<li>Indices based on patch dimension:
<ul>
<li> <a href="r.li.mps.html">r.li.mps</a>: Calculates mean patch size index on a raster map, using a 4 neighbour algorithm</li>
<li> <a href="r.li.padcv.html">r.li.padcv</a>: Calculates coefficient of variation of patch area on a raster map</li>
<li> <a href="r.li.padrange.html">r.li.padrange</a>: Calculates range of patch area size on a raster map</li>
<li> <a href="r.li.padsd.html">r.li.padsd</a>: Calculates standard deviation of patch area a raster map</li>
</ul>

<li>Indices based on patch shape:
<ul>
<li> <a href="r.li.shape.html">r.li.shape</a>: Calculates shape index on a raster map</li>
</ul>

<li>Indices based on patch edge: <!-- border? -->
<ul>
<li> <a href="r.li.edgedensity.html">r.li.edgedensity</a>: Calculates edge density index on a raster map, using a 4 neighbour algorithm</li>
</ul>

<li>Indices based on patch attributes:
<ul>
<li> <a href="r.li.cwed.html">r.li.cwed</a>: Calculates contrast Weighted Edge Density index on a raster map</li>
<li> <a href="r.li.mpa.html">r.li.mpa</a>: Calculates mean pixel attribute index on a raster map</li>
</ul>

</ul>

<b>Diversity indices</b>:
Expand All @@ -159,27 +180,45 @@ <h2>SEE ALSO</h2>
<li> <a href="r.li.simpson.html">r.li.simpson</a>: Calculates Simpson diversity index on a raster map</li>
</ul>


<h2>ADDING NEW INDICES</h2>
New indices can be defined and implemented by any C programmer, without having to
deal with all basic functions (IO etc.). The computing architecture and the functions
are clearly separated, thus allowing an easy expandability. Every index is defined
separately, placed in a directory along with its Makefile for compiling it and a file
description.html which describes the index including a simple example of use.

New indices can be defined and implemented by any C programmer, without
having to deal with all basic functions (IO etc.). The computing
architecture and the functions are clearly separated, thus allowing an
easy expandability. Every index is defined separately, placed in a
directory along with its Makefile for compiling it and a file
&lt;module_name&gt;.html which describes the index including a simple
example of use.


<h2>REFERENCES</h2>

McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
analysis program for quantifying landscape structure. USDA For. Serv.
Gen. Tech. Rep. PNW-351 (<a href="http://www.fs.fed.us/pnw/pubs/gtr_351.pdf">PDF</a>).
Gen. Tech. Rep. PNW-351
(<a href="http://www.fs.fed.us/pnw/pubs/gtr_351.pdf">PDF</a>).


<h2>AUTHORS</h2>

<a href="mailto:[email protected]">Claudio Porta</a> and
<a href="mailto:[email protected]">Lucio Davide Spano</a>, students of Computer Science
University of Pisa (Italy). <br>
<a href="mailto:[email protected]">Lucio Davide Spano</a>,
students of Computer Science
University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI)<br>

<p><i>Last changed: $Date$</i>
<p>
<i>Last changed: $Date$</i>

<hr>
<p><a href="index.html">Main index</a> - <a href="raster.html">Raster index</a> - <a href="topics.html">Topics index</a> - <a href="keywords.html">Keywords Index</a> - <a href="full_index.html">Full index</a>

<p>
<a href="index.html">Main index</a>
- <a href="raster.html">Raster index</a>
- <a href="topics.html">Topics index</a>
- <a href="keywords.html">Keywords Index</a>
- <a href="full_index.html">Full index</a>

</body>
</html>

0 comments on commit 87a78c8

Please sign in to comment.