r.li.* manuals: cosmetics

git-svn-id: https://svn.osgeo.org/grass/grass/trunk@59002 15284696-431f-4ddb-bdfa-cd5b030d7da7

gui/wxpython/rlisetup/g.gui.rlisetup.html

@@ -2,20 +2,32 @@
 <!-- meta page index: wxGUI -->
 <h2>DESCRIPTION</h2>
 
-The <b>RLi Setup</b> is a <em><a href="wxGUI.html">wxGUI</a></em>
+The <b>g.gui.rlisetup</b> is a <em><a href="wxGUI.html">wxGUI</a></em>
 component which allows the user to create a configuration file
-for <em>r.li</em> modules.
+for the analytical <em>r.li</em> modules. For a general introduction, see 
+<a href="r.li.html">r.li</a>.
+<br>
+The configurations are raster map independent, it means that you can use
+a file created on a raster map for analyze any other you have. <br>
+The program is completely interactive and uses a GUI to help you 
+in your choices.
+<p>
+TODO: merge in material from GRASS GIS 6 (raster/r.li/r.li.setup/r.li.setup.html)
+
+<h2>NOTES</h2>
 
-<!-- TODO: merge in material from raster/r.li/r.li.setup/r.li.setup.html -->
+Configuration files are raster map independent because areas are saved using
+relative coordinates.
 
 <h2>EXAMPLES</h2>
 
 <h3>Moving window analysis on full region</h3>
 
-<i>TODO: update to new g.gui dialog:</i>
-
-Example for a 7x7 moving window analysis on full region:
-
+<i>TODO: update examples to new g.gui.rlisetup dialog:</i>
+<p>
+Example for a 7x7 moving window analysis on full region, the output 
+is a raster map:
+<p>
 Click on "New", then:
 <ul>
  <li> Configuration file name: "movwindow7"</li>
@@ -47,43 +59,79 @@ Select type of shape:
 <p>
 Now an anaysis can be performed using one of the analytical modules, e.g.
 <div class="code"><pre>
+g.region rast=forests -p
 r.li.patchdensity input=forests conf=movwindow7 output=forests_p_dens7
+r.univar forests_p_dens7
 </pre></div>
 
-The result is a new raster map "forests_p_dens7".
+The result is the new raster map "forests_p_dens7" which shows (in this example)
+the patch density of the forest areas.
 <br>
 See the respective modules for further examples.
 
-<!-- TODO: add configuration example which results in ASCII output rather than raster map -->
 
-<h2>NOTES</h2>
+<h3>Whole region analysis</h3>
+
+<!-- TODO: find a better example and briefly explain the meaning of result --> 
+Example for a whole region analysis, the output is a text file:
+
+Click on "New", then:
+<ul>
+ <li> Configuration file name: "whole_region"</li>
+ <li> Raster map name to use to select areas: "lsat7_2000_40"</li>
+</ul>
 
-Configuration files are raster map independent because areas are
-saved using relative coordinates.
+1. Setup sampling frame:
+<ul>
+<li> Define a sampling frame (region for analysis): "Whole map layer", then "OK"</li>
+</ul>
+
+2. Setup sampling frame
+<ul>
+<li> Define sampling areas: "Whole map layer", then "OK"</li>
+</ul>
+
+3. Save settings: click on button
+<br>
+(4.) Close
+<p>
+Now an anaysis can be performed using one of the analytical modules, e.g.
+<div class="code"><pre>
+g.region rast=lsat7_2002_40 -p
+r.li.shannon input=lsat7_2000_40 conf=whole_region output=lsat7_2000_40_shannon
+</pre></div>
+
+The result is the new text file "forests_p_dens7" (stored in folder <tt>$HOME/.r.li/output/</tt>.
+<br>
+See the respective modules for further examples.
 
 
 <h2>SEE ALSO</h2>
 
 <em>
-  <a href="wxGUI.html">wxGUI</a><br>
-  <a href="wxGUI.components.html">wxGUI components</a>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.daemon.html">r.li.daemon</a>
+</em>
+<p>
+<em>
+<a href="http://grass.osgeo.org/gdp/landscape/r_le_manual5.pdf">Old r.le suite manual</a>
 </em>
-
 <p>
 <em>
-  <a href="g.gui.html">g.gui</a>,
-  <a href="g.gui.animation.html">g.gui.animation</a>,
-  <a href="g.gui.dbmgr.html">g.gui.dbmgr</a>,
-  <a href="g.gui.gmodeler.html">g.gui.gmodeler</a>,
-  <a href="g.gui.iclass.html">g.gui.iclass</a>,
-  <a href="g.gui.mapswipe.html">g.gui.mapswipe</a>,
-  <a href="g.gui.psmap.html">g.gui.psmap</a>,
-  <a href="g.gui.vdigit.html">g.gui.vdigit</a>
+  <a href="wxGUI.html">wxGUI</a><br>
+  <a href="wxGUI.components.html">wxGUI components</a>
 </em>
 
+
+<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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
+
 <h2>AUTHOR</h2>
 
-Luca Delucchi
+Luca Delucchi<br>
+Rewritten from <em>r.li.setup</em> by Claudio Porta and Lucio Davide Spano
 
 <p>
 <i>$Date$</i>

raster/r.li/r.li.cwed/r.li.cwed.html

@@ -25,7 +25,7 @@ consider in the calculation. Each row must be saved using this syntax:<br>
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values it is considered to

raster/r.li/r.li.dominance/r.li.dominance.html

@@ -15,7 +15,7 @@ with:
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.dominance</em>

raster/r.li/r.li.edgedensity/r.li.edgedensity.html

@@ -23,7 +23,7 @@
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.edgedensity</em>

raster/r.li/r.li.html

@@ -21,6 +21,7 @@ raster, landscape structure analysis, overview, landscape metrics, landscape pat
 <h2>DESCRIPTION</h2>
 
 The <em>r.li</em> suite is a toolset for multiscale analysis of landscape structure.
+<!-- rephrase reference to r.le which is long time ago ...-->
 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).
@@ -63,29 +64,31 @@ The general procedure to calculate an index from a raster map is two-fold:
 The <em>r.li.daemon</em> module also has a "main" function front-end
 which can be run, but it is only a template for development of new
 indices so not built by default.
-<!-- mhh ??: -->
+<!-- mhh ??: 
 The function itself has no meaning, it is only useful as an example and 
-for debugging. 
-
+for debugging.
+-->
 
 <h2>EXAMPLE</h2>
 
 Calculate a patch density index on the entire 'geology' raster map
 in the Spearfish sample dataset, using a 5x5 moving window:
 
+<!-- TODO: update to new wxGUI: -->
+
 <ol>
 <li> CREATE A NEW CONFIGURATION FILE
   <ol>
   <li> run 
 <div class="code"><pre>
-  r.li.setup
+  g.gui.rlisetup
 </pre></div>
   <li> The main <em>r.li.setup</em> window is displayed, click on "New"
   <li> The new configuration window is now displayed, enter the
 	configuration file name (e.g., "my_conf", do not use absolute paths)
   
-  Now it is displayed the new configuration window,
-	enter the configuration file name (e.g., "my_conf", do not use absolute paths) 
+  Now the new configuration window is displayed.
+	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 map layer" and click "OK"
@@ -202,9 +205,7 @@ Gen. Tech. Rep. PNW-351
 
 <h2>AUTHORS</h2>
 
-<a href="mailto:porta@cli.di.unipi.it">Claudio Porta</a> and 
-<a href="mailto:spano@cli.di.unipi.it">Lucio Davide Spano</a>,
- students of Computer Science 
+Claudio Porta and Lucio Davide Spano, students of Computer Science,
 University of Pisa (Italy).<br>
 Commission from Faunalia Pontedera (PI)<br>
 
@@ -217,6 +218,6 @@ Commission from Faunalia Pontedera (PI)<br>
  - <a href="topics.html">Topics index</a>
  - <a href="keywords.html">Keywords Index</a>
  - <a href="full_index.html">Full index</a>
-<p>&copy; 2003-2014 <a href="http://grass.osgeo.org">GRASS Development Team</a>, GRASS GIS 7.0.svn Reference Manual</p>
+<p>&copy; 2008-2014 <a href="http://grass.osgeo.org">GRASS Development Team</a>, GRASS GIS 7.0.svn Reference Manual</p>
 </body>
 </html>

raster/r.li/r.li.mpa/r.li.mpa.html

@@ -16,7 +16,7 @@ with:<br>
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.mpa</em> considers to

raster/r.li/r.li.mps/r.li.mps.html

@@ -15,7 +15,7 @@ with:
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster contains NULL value cells, <em>r.li.mps</em>

raster/r.li/r.li.padcv/r.li.padcv.html

@@ -17,7 +17,7 @@ with:<br>
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 If input raster is not full of null values <em>r.li.padcv</em> returns a value &gt;=0 that is PADcv. <br>
 If the input raster map contains only NULL values then <em>r.li.padcv</em> returns -1. <br>

raster/r.li/r.li.padrange/r.li.padrange.html

@@ -14,7 +14,7 @@ with:<br>
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.padrange</em>

raster/r.li/r.li.padsd/r.li.padsd.html

@@ -14,7 +14,7 @@ with:<br>
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 If input raster is not full of null values <em>r.li.padsd</em> returns a
 value >=0 that is PADsd. <br>

raster/r.li/r.li.patchdensity/r.li.patchdensity.html

@@ -13,7 +13,7 @@ This index is calculated using a 4 neighbour algorithm.
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 A map of NULL values is considered to have zero patches. <br>

raster/r.li/r.li.patchnum/r.li.patchnum.html

@@ -9,7 +9,7 @@ This index is calculated using a 4 neighbour algorithm<br>
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO verify: -->
 If the input raster map contains only NULL values then it is considered to have zero patch. <br>

raster/r.li/r.li.pielou/r.li.pielou.html

@@ -14,7 +14,7 @@ with:
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 If the input raster contains NULL value cells, <em>r.li.pielou</em>
 returns -1 for these cells. <br>

raster/r.li/r.li.renyi/r.li.renyi.html

@@ -16,7 +16,7 @@ with:
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.renyi</em>

raster/r.li/r.li.richness/r.li.richness.html

@@ -12,7 +12,7 @@ with:
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.richness</em>

raster/r.li/r.li.setup/r.li.setup.html

@@ -1,7 +1,7 @@
 <h2>DESCRIPTION</h2>
 
 <em>r.li.setup</em>  creates and shows configuration files for the 
-others <em>r.li</em> modules. For a general introduction, see 
+other analytical <em>r.li</em> modules. For a general introduction, see 
 <a href="r.li.html">r.li</a>.
 <br>
 The configurations are raster map independent, 
@@ -49,11 +49,11 @@ The startup window shows your configuration files, you can:
  rectangles with differents colors (green for the raster map, red for 
  the sample frame and blue for the sample areas), and other notes 
  (disposition of sample areas etc). The configuration file is saved 
- in <tt>~/.r.li/history/my_conf</tt> (the file name can be defined by 
+ in <tt>$HOME/.grass7/r.li/my_conf</tt> (the file name can be defined by 
  the user). The output can either be a new raster map (in case of 
  using a "moving window" analysis) or be an ASCII text file (when not 
  performing a "moving window" analysis) containing the result which 
- is then saved to the folder <tt>~/.grass7/r.li/output/</tt>.
+ is then saved to the folder <tt>$HOME/.grass7/r.li/output/</tt>.
  <br>
  <!-- TODO: applies to all output or only ASCII output?? -->
  All dimensions are percentages of raster rows or columns.</li>
@@ -143,18 +143,22 @@ The startup window shows your configuration files, you can:
   <li><em><b>Close</b></em> module window.</li>
 </ol>
 
+<h2>NOTES</h2>
+
+Configuration files are raster map independent because areas are saved using
+relative coordinates.
+
 <h2>EXAMPLES</h2>
 
 <h3>Moving window analysis on full region</h3>
 
-Example for a 7x7 moving window analysis on full region:
-
+Example for a 7x7 moving window analysis on full region, the output 
+is a raster map:
+<p>
+Click on "New", then:
 <ul>
-<li> Click on "New"</li>
- <ul>
-  <li> Configuration file name: "movwindow7"</li>
-  <li> Raster map name to use to select areas: "forests"</li>
- </ul>
+ <li> Configuration file name: "movwindow7"</li>
+ <li> Raster map name to use to select areas: "forests"</li>
 </ul>
 
 1. Setup sampling frame:
@@ -166,15 +170,14 @@ Example for a 7x7 moving window analysis on full region:
 <ul>
 <li> Define sampling areas: "Moving window", then "OK"</li>
 <li> Then click on "Use keyboard to define moving window dimension"</li>
+</ul>
+
+Select type of shape:
 <ul>
- <li>Select type of shape</li>
- <ul>
-  <li> [x] Rectangular</li>
-  <li> Width size (in cells)?: "7"</li>
-  <li> Height size (in cells)?: "7"</li>
-  <li> Then "Save settings"</li>
- </ul>
- </ul>
+<li> [x] Rectangular</li>
+<li> Width size (in cells)?: "7"</li>
+<li> Height size (in cells)?: "7"</li>
+<li> Then "Save settings"</li>
 </ul>
 
 3. Save settings: click on button
@@ -183,19 +186,51 @@ Example for a 7x7 moving window analysis on full region:
 <p>
 Now an anaysis can be performed using one of the analytical modules, e.g.
 <div class="code"><pre>
+g.region rast=forests -p
 r.li.patchdensity input=forests conf=movwindow7 output=forests_p_dens7
+r.univar forests_p_dens7
 </pre></div>
 
-The result is a new raster map "forests_p_dens7".
+The result is the new raster map "forests_p_dens7" which shows (in this example)
+the patch density of the forest areas.
 <br>
 See the respective modules for further examples.
 
-<!-- TODO: add configuration example which results in ASCII output rather than raster map -->
 
-<h2>NOTES</h2>
+<h3>Whole region analysis</h3>
 
-Configuration files are raster map independent because areas are saved using 
-relative coordinates.
+<!-- TODO: find a better example and briefly explain the meaning of result --> 
+Example for a whole region analysis, the output is a text file:
+
+Click on "New", then:
+<ul>
+ <li> Configuration file name: "whole_region"</li>
+ <li> Raster map name to use to select areas: "lsat7_2000_40"</li>
+</ul>
+
+1. Setup sampling frame:
+<ul>
+<li> Define a sampling frame (region for analysis): "Whole map layer", then "OK"</li>
+</ul>
+
+2. Setup sampling frame
+<ul>
+<li> Define sampling areas: "Whole map layer", then "OK"</li>
+</ul>
+
+3. Save settings: click on button
+<br>
+(4.) Close
+<p>
+Now an anaysis can be performed using one of the analytical modules, e.g.
+<div class="code"><pre>
+g.region rast=lsat7_2002_40 -p
+r.li.shannon input=lsat7_2000_40 conf=whole_region output=lsat7_2000_40_shannon
+</pre></div>
+
+The result is the new text file "forests_p_dens7" (stored in folder <tt>$HOME/.r.li/output/</tt>.
+<br>
+See the respective modules for further examples.
 
 
 <h2>SEE ALSO</h2>
@@ -219,7 +254,7 @@ Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a
 Claudio Porta and Lucio Davide Spano, students of Computer Science<br>
 University of Pisa (Italy).<br>
 Commission from Faunalia Pontedera (PI)<br>
-Rebuild of <em>r.le.setup</em> from William L. Baker
+Rewritten from <em>r.le.setup</em> by William L. Baker
 
 <p>
 <i>Last changed: $Date$</i>

raster/r.li/r.li.shannon/r.li.shannon.html

@@ -15,7 +15,7 @@ with:
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.shannon</em>

raster/r.li/r.li.shape/r.li.shape.html

@@ -8,7 +8,7 @@
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.shape</em>

raster/r.li/r.li.simpson/r.li.simpson.html

@@ -15,7 +15,7 @@ with:
 Do not use absolute path names for the <b>output</b> map/file.
 If the "moving window" method was selected in <b>r.li.setup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>~/.grass7/r.li/output/</tt> folder.
+the <tt>$HOME/.grass7/r.li/output/</tt> folder.
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.simpson</em>