sync with devbr6 up to https://trac.osgeo.org/grass/changeset/58899

git-svn-id: https://svn.osgeo.org/grass/grass/trunk@58963 15284696-431f-4ddb-bdfa-cd5b030d7da7

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

@@ -38,6 +38,7 @@ after index calculation.<br>
 
 
 <h2>EXAMPLES</h2>
+
 To calculate mean pixel attribute index on map my_map, using
 my_conf configuration file and saving results in
 my_out file run:<br>
@@ -51,18 +52,23 @@ r.li.cwed input=my_map conf=my_conf path=my_file output=my_out
 56,12,0.54<br>
 23,66,0.99<br>
 
+
 <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.
 
+
 <h2>SEE ALSO</h2>
 
 <em><a href="r.li.html">r.li</a></em> package overview <br>
 <em><a href="r.li.daemon.html">r.li.daemon</a></em><br>
 <em><a href="r.li.setup.html">r.li.setup</a></em>
 
+
 <h2>AUTHORS</h2>
+
 Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
 Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
 

raster/r.li/r.li.daemon/daemon.c

@@ -52,7 +52,7 @@ int calculateIndex(char *file, int f(int, char **, struct area_entry *, double *
     int res;
     int i, doneDir, mv_fd, random_access;
 
-    /*int mv_rows, mv_cols; */
+    /* int mv_rows, mv_cols; */
     struct list *l;
     msg m, doneJob;
 
@@ -152,7 +152,8 @@ int calculateIndex(char *file, int f(int, char **, struct area_entry *, double *
 		error_Output(res, doneJob);
 	    }
 	    else {
-		/*printf("todo ");fflush(stdout); *//* TODO scrivere su raster NULL ??? */
+		/* printf("todo "); fflush(stdout); */
+		/* TODO write to raster NULL ??? */
 	    }
 	}
     }

raster/r.li/r.li.daemon/daemon.h

@@ -23,9 +23,6 @@
 #include "defs.h"
 
 
-/**
- * \brief number of r.li.workers to use
- */
 #define NORMAL 1
 #define MVWIN 2
 #define GEN 3

raster/r.li/r.li.daemon/r.li.daemon.html

@@ -32,12 +32,13 @@ To write a new index only two steps are needed:
 	folder, which contains all index declarations. This function must be of this kind:
 	<br><div class="code"><pre>
         int index(int fd, char ** par, area_des ad, double * result)
-	</pre></div><br>
+	</pre></div>
+	<br>
 	where: <ul>
-			<li><i>fd</i> is the raster map descriptor
-			<li><i>par</i> is a matrix for special parameter (like argv in main)
-			<li><i>ad</i> is the area descriptor 
-			<li><i>result</i> is where to put the index calculation result
+		    <li><i>fd</i> is the raster map descriptor
+		    <li><i>par</i> is a matrix for special parameter (like argv in main)
+		    <li><i>ad</i> is the area descriptor 
+		    <li><i>result</i> is where to put the index calculation result
 		</ul>
 	This function has to return 1 on success and 0 otherwise. <br><br>
 	<li>
@@ -57,6 +58,7 @@ To write a new index only two steps are needed:
 </ol>
 Compile it using a changed Makefile based on the file for <em>r.li.patchdensity</em>.
 
+
 <h2>NOTES</h2>
 
 Using GRASS library function to access raster rows can slow down moving windows 
@@ -69,6 +71,7 @@ RLI_get_dcell_row(int, int, area_des)
 to use an ad hoc build memory management developed to speed up the system.
 The documentation is in doxygen files.
 
+
 <h2>SEE ALSO</h2>
 
 <em><a href="http://grass.osgeo.org/gdp/landscape/r_le_manual5.pdf">old r.le manual</a></em><br>
@@ -82,6 +85,7 @@ 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>AUTHORS</h2>
 
 Claudio Porta and Lucio Davide Spano, students of Computer Science 
@@ -95,6 +99,11 @@ Read the COPYING file that comes with GRASS for details.
 <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>

raster/r.li/r.li.edgedensity/edgedensity.c

@@ -55,8 +55,9 @@ int main(int argc, char *argv[])
     class->type = TYPE_STRING;
     class->required = NO;
     class->multiple = NO;
-    class->description =
-	"The value of the patch type, it can be integer, double or float; it will be changed in function of map type";
+    class->label = _("The value of the patch type");
+    class->description = _("It can be integer, double or float; "
+			   "it will be changed in function of map type");
 
 
     if (G_parser(argc, argv))
@@ -119,24 +120,18 @@ int calculate(int fd, struct area_entry *ad, char **valore, double *result)
     double e = 0;
     double somma = 0;
     double area = 0;
-
     CELL *buf_corr, *buf_sup, *buf_inf;
     CELL prevCell, corrCell, supCell, infCell, nextCell;
-
     AVL_table *array;
-
     long tot = 0;
     long zero = 0;
     long m = 0;
     long bordoCorr = 0;
-
     avl_tree albero = NULL;
-
     int i, j;
     int mask_fd = -1, *mask_corr, *mask_sup, *mask_inf;
     int masked = FALSE;
     int ris;
-
     generic_cell c1;
 
     buf_sup = NULL;
@@ -145,8 +140,8 @@ int calculate(int fd, struct area_entry *ad, char **valore, double *result)
     /* open mask if needed */
     if (ad->mask == 1) {
 	if ((mask_fd = open(ad->mask_name, O_RDONLY, 0755)) < 0) {
-	    G_fatal_error("can't  open mask %s", ad->mask_name);
-	    return RLI_ERRORE;
+	    G_fatal_error("Cannot open mask file <%s>", ad->mask_name);
+	    return RLI_ERRORE;  /* FIXME: can not return from a fatal error */
 	}
 
 	mask_corr = G_malloc(ad->cl * sizeof(int));
@@ -173,9 +168,11 @@ int calculate(int fd, struct area_entry *ad, char **valore, double *result)
     /* the first time buf_sup is all null */
     Rast_set_c_null_value(buf_sup + ad->x, ad->cl);
 
-    for (j = 0; j < ad->rl; j++) {	/* for each raster row */
+    /* for each raster row */
+    for (j = 0; j < ad->rl; j++) {
 
-	buf_corr = RLI_get_cell_raster_row(fd, j + ad->y, ad);	/* read row of raster */
+	/* read row of raster */
+	buf_corr = RLI_get_cell_raster_row(fd, j + ad->y, ad);
 
 	if (j > 0)		/* not first row */
 	    buf_sup = RLI_get_cell_raster_row(fd, j - 1 + ad->y, ad);
@@ -398,8 +395,8 @@ int calculateD(int fd, struct area_entry *ad, char **valore, double *result)
     /* open mask if needed */
     if (ad->mask == 1) {
 	if ((mask_fd = open(ad->mask_name, O_RDONLY, 0755)) < 0) {
-	    G_fatal_error("can't  open mask");
-	    return RLI_ERRORE;
+	    G_fatal_error("Cannot open mask file");
+	    return RLI_ERRORE;  /* FIXME: can not return from a fatal error */
 	}
 
 	mask_corr = G_malloc(ad->cl * sizeof(int));
@@ -651,8 +648,8 @@ int calculateF(int fd, struct area_entry *ad, char **valore, double *result)
     /* open mask if needed */
     if (ad->mask == 1) {
 	if ((mask_fd = open(ad->mask_name, O_RDONLY, 0755)) < 0) {
-	    G_fatal_error("can't  open mask");
-	    return RLI_ERRORE;
+	    G_fatal_error("Cannot open mask file");
+	    return RLI_ERRORE;  /* FIXME: can not return from a fatal error */
 	}
 
 	mask_corr = G_malloc(ad->cl * sizeof(int));

raster/r.li/r.li.html

@@ -33,7 +33,7 @@ raster map whose cell values are integer (e.g., 1, 2) or floating point
 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
+window of square, rectangular or 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
@@ -52,21 +52,26 @@ The general procedure to calculate an index from a raster map is two-fold:
 <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 one or more of the <em>r.li.<b>[index]</b></em> modules (e.g.,
+    <em>r.li.<b>patchdensity</b></em>) to 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.
+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 ??: -->
-The function itself has no meaning, it can be used only for debug.
+The function itself has no meaning, it is only useful as an example and 
+for debugging. 
+
 
 <h2>EXAMPLE</h2>
 
-To calculate a patch density index on a whole 'geology' raster map in the
-Spearfish region, using a 5x5 moving window, follow this procedure:
+Calculate a patch density index on the entire 'geology' raster map
+in the Spearfish sample dataset, using a 5x5 moving window:
 
 <ol>
 <li> CREATE A NEW CONFIGURATION FILE
@@ -76,14 +81,17 @@ Spearfish region, using a 5x5 moving window, follow this procedure:
   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,
+  <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) 
 	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 frame", select "Whole map layer" 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> Select "Rectangle" and enter 5 in the "height" and "width" fields
   <li> Click on "Save settings"
   <li> Close the <em>r.li.setup</em> window
   </ol>

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

@@ -44,7 +44,7 @@ Example for Spearfish forest areas:
 g.region rast=landcover.30m -p
 # extract forested areas:
 r.category landcover.30m
-r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <=43,1,null())"
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43, 1, null())"
 
 # patch density (7x7 moving window defined in r.li.setup):
 r.li.patchdensity forests conf=movwindow7 out=forests_p_dens7

raster/r.li/r.li.setup/masked_area_selection.sh

@@ -1,76 +1,88 @@
 #!/bin/sh
-#%Module 
+#
+# Masked area selection using r.digit
+#
+
+#%Module
 #%description: Select a circular or polygonal area
 #%End
 #%option
 #% key: raster
 #% type: string
-#% description: raster map to to analyse
+#% description: Raster map to to analyse
 #% required: yes
 #%end
 #%option
 #% key: vector
 #% type: string
-#% description: vector to overlay
+#% description: Vector map to overlay
 #% required: no
 #%end
 #%option
 #% key: site
 #% type: string
-#% description: site to overlay
+#% description: Vector points map to overlay
 #% required: no
 #%end
 #%option
 #% key: config
 #% type: string
-#% description: name of configuration file where insert areas
+#% description: Name of configuration file where insert areas
 #% required: yes
 #%end
 #%option
 #% key: north
 #% type: string
-#% description: nothern edge (use only with f flag)
+#% description: Northern edge (use only with the 'f' flag)
 #% required: no
 #%end
 #%option
 #% key: south
 #% type: string
-#% description:south edge (use only with f flag)
+#% description: Southern edge (use only with the 'f' flag)
 #% required: no
 #%end
 #%option
 #% key: east
 #% type: string
-#% description: east edge(use only with f flag)
+#% description: Eastern edge (use only with the 'f' flag)
 #% required: no
 #%end
 #%option
 #% key: west 
 #% type: string
-#% description: west edge(use only with f flag)
+#% description: Western edge (use only with the 'f' flag)
 #% required: no
 #%end
 #%flag
 #% key: f
-#% description: sample frame yet selected 
+#% description: Sample frame not yet selected, set from module options
 #%end
 #%flag
 #% key: c
-#% description: take a circular area
+#% description: Take a circular area
 #%end
 
 # Where to find the others scripts
 f_path="$GISBASE/etc/r.li.setup"
 
-# Check if we have grass
+# Check if we are in a GRASS session
 if test "$GISBASE" = ""; then
- echo "You must be in GRASS GIS to run this program." >&2
- exit 1
+   echo "You must be in GRASS GIS to run this program." 1>&2
+   exit 1
  fi
 if [ "$1" != "@ARGS_PARSED@" ] ; then
-  exec g.parser "$0" "$@"
+   exec g.parser "$0" "$@"
 fi
 
+
+#### environment variables
+GISDBASE=`g.gisenv get=GISDBASE`
+LOCATION=`g.gisenv get=LOCATION_NAME`
+MAPSET=`g.gisenv get=MAPSET`
+: ${GISDBASE?} ${LOCATION?} ${MAPSET?}
+
+
 #### set temporary files
 TMP="`g.tempfile pid=$$`"
 if [ $? -ne 0 ] || [ -z "$TMP" ] ; then
@@ -79,46 +91,46 @@ if [ $? -ne 0 ] || [ -z "$TMP" ] ; then
 fi
 
 
-#### environment variables
-g.gisenv LOCATION_NAME > $TMP.var
-read LOCATION < $TMP.var
-g.gisenv GISDBASE > $TMP.var
-read GISDBASE < $TMP.var
-g.gisenv MAPSET > $TMP.var
-read MAPSET < $TMP.var
-# show the sampling frame
+# FIXME: use WIND_OVERRIDE
 
-if [ $GIS_FLAG_f -eq 1 ] ; then
-    g.region n=$GIS_OPT_north s=$GIS_OPT_south e=$GIS_OPT_east w=$GIS_OPT_west
+# show the sampling frame
+if [ "$GIS_FLAG_f" -eq 1 ] ; then
+    g.region n="$GIS_OPT_north" s="$GIS_OPT_south" e="$GIS_OPT_east" w="$GIS_OPT_west"
 else
-    g.region rast=$GIS_OPT_raster
+    g.region rast="$GIS_OPT_raster"
 fi
-# open x1 monitor
+
+# open x1 Xmonitor
 d.mon stop=x1
 d.mon start=x1
 
-d.rast -o map=$GIS_OPT_raster
+d.rast -o map="$GIS_OPT_raster"
+
 if [ -n "$GIS_OPT_vector" ] ; then
-    d.vect map=$GIS_OPT_vector
+    d.vect map="$GIS_OPT_vector"
 fi
 if [ -n "$GIS_OPT_site" ] ; then 
-    d.vect  map=$GIS_OPT_site
+    d.vect map="$GIS_OPT_site"
 fi
-#let draw area
-if [ $GIS_FLAG_c -eq 1 ] ; then
-    cp $f_path/circle.txt $$.txt 
-    echo "$$" >> $$.txt 
+
+# setup for drawing area
+if [ "$GIS_FLAG_c" -eq 1 ] ; then
+   RDIG_INSTR="$f_path/circle.txt"
 else
-    cp $f_path/polygon.txt  $$.txt 
-    echo "$$" >> $$.txt
+   RDIG_INSTR="$f_path/polygon.txt"
 fi
- 
-r.digit < $$.txt
 
-#show the selected area
-d.rast -o map=$$ 
-export name=$$.val
-$GRASS_WISH $f_path/area_query 
+# feed options to r.digit
+r.digit output="tmp_rli_mask.$$" < "$RDIG_INSTR"
+
+
+# show the selected area
+d.rast -o map="tmp_rli_mask.$$"
+
+name=$$.val
+export name
+
+"$GRASS_WISH" "$f_path/area_query"
     cat $name | cut -f1 -d ' ' > $name.var
     read ok < $name.var
     cat $name | cut -f2 -d' ' > $name.var
@@ -162,6 +174,9 @@ $GRASS_WISH $f_path/area_query
     fi
 
 d.mon stop=x1
-#clean tmp files
-rm -f $$*
-rm -f $TMP*
+
+# clean tmp files
+#FIXME: use g.tempfile
+rm -f "$$"*
+rm -f "$TMP"*
+

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

@@ -5,7 +5,6 @@
 # MODULE:       r.li.setup
 #
 # AUTHOR(S):    Spano Lucio Davide & Claudio Porta
-#          
 #
 # PURPOSE:     Configuration editor for r.li.<index>. It sets sampling frame and 
 #              sample areas to analyze, the configuration is raster map indipendent.
@@ -14,22 +13,43 @@
 # Read the COPYING file that comes with GRASS for details.
 #
 #############################################################################
+
 #%Module
 #%  description: Configuration editor for r.li.'index'
 #%  keywords: raster, landscape structure analysis
 #%End
 
 if  [ -z "$GISBASE" ] ; then
-   echo "You must be in GRASS GIS to run this program."
+   echo "You must be in GRASS GIS to run this program." 1>&2
    exit 1
 fi
 
+
+cleanup()
+{
+   # remove temporary region
+   eval `g.findfile elem=windows file="tmp_rlisetup.$$" | grep '^name='`
+   if [ -n "$name" ] ; then
+      unset WIND_OVERRIDE
+      g.remove region="tmp_rlisetup.$$" --quiet
+   fi
+}
+trap "cleanup" 2 3 15
+
+
 if [ $# -eq 0 ] ; then
-   $GISBASE/etc/r.li.setup/r.li.setup.main
+   # setup internal region
+   g.region save="tmp_rlisetup.$$"
+   WIND_OVERRIDE="tmp_rlisetup.$$"
+   export WIND_OVERRIDE
+
+   "$GISBASE"/etc/r.li.setup/r.li.setup.main
+
+   cleanup
    exit 0
 fi
 
+
 if [ "$1" != "@ARGS_PARSED@" ] ; then
-  exec g.parser "$0" "$@"
+   exec g.parser "$0" "$@"
 fi
-

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

@@ -47,10 +47,11 @@ 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>~/.grass7/r.li/my_conf</tt>.
+The configuration file is saved in <tt>~/.grass7/r.li/my_conf</tt>
+(the file name can be defined by the user).
 <!-- NOT REALLY CLEAR: -->
 Configuration output files are raster if moving window disposition was
-selected, otherwise they are in ~/.r.li/output folder.
+selected, otherwise they are in <tt>~/.r.li/output</tt> folder.
 <br> 
 All dimension are percentage of raster rows or columns.
 <li><em><b>Create a new file:</b></em> this create a new configuration 

raster/r.li/r.li.setup/sample_area_vector.sh

@@ -2,131 +2,153 @@
 #
 # This program is free software under the GPL (>=v2)
 # Read the COPYING file that comes with GRASS for details.
+#
 
-#%Module 
-#% description: Create sample area from a vector map 
+#%Module
+#% description: Create sample area from a vector map
 #%End
 #%option
 #% key: raster
 #% type: string
-#% description: raster map to to analyse
+#% gisprompt: old,cell,raster
+#% key_desc: name
+#% description: Raster map to to analyse
 #% required: yes
 #%end
 #%option
 #% key: vector
 #% type: string
-#% description: vector map where areas are defined
+#% gisprompt: old,vector,vector
+#% key_desc: name
+#% description: Vector map where areas are defined
 #% required: yes
 #%end
 #%option
 #% key: config
 #% type: string
-#% description: name of configuration file where insert areas
+#% key_desc: name
+#% gisprompt: new_file,file,output
+#% description: Name of configuration file where areas are to be saved
 #% required: yes
 #%end
 
 
-# Check if we have grass
-if test "$GISBASE" = ""; then
- echo "You must be in GRASS GIS to run this program." >&2
- exit 1
- fi
+# Check if we are in a GRASS session
+if [ -z "$GISBASE" ] ; then
+   echo "You must be in GRASS GIS to run this program." 1>&2
+   exit 1
+fi
+
 if [ "$1" != "@ARGS_PARSED@" ] ; then
-  exec g.parser "$0" "$@"
+   exec g.parser "$0" "$@"
 fi
+
 #### set temporary files
 TMP="`g.tempfile pid=$$`"
 if [ $? -ne 0 ] || [ -z "$TMP" ] ; then
-    echo "ERROR: unable to create temporary files" 1>&2
-    exit 1
+   echo "ERROR: unable to create temporary files" 1>&2
+   exit 1
 fi
+
 #### environment variables
-g.gisenv LOCATION_NAME > $TMP.var
-read LOCATION < $TMP.var
-g.gisenv GISDBASE > $TMP.var
-read GISDBASE < $TMP.var
-g.gisenv MAPSET > $TMP.var
-read MAPSET < $TMP.var
+GISDBASE=`g.gisenv get=GISDBASE`
+LOCATION=`g.gisenv get=LOCATION_NAME`
+MAPSET=`g.gisenv get=MAPSET`
+: ${GISDBASE?} ${LOCATION?} ${MAPSET?}
 
 f_path="$GISBASE/etc/r.li.setup"
 
 ##############################################################
-#read categories from input vector, extract,
-#convert to raster and save the bounds to configuration file
+# read categories from input vector, extract,
+# convert to raster and save the bounds to configuration file
 ##############################################################
 
-#using v.category instead of v.build with cdump
-v.category input=$GIS_OPT_vector option=print > $TMP.cat
+# using v.category instead of v.build with cdump
+v.category input=$GIS_OPT_vector option=print | sort | uniq > "$TMP.cat"
 
-#get input vector name
+# get input vector name
 GIS_OPT_input_vector=`echo $GIS_OPT_vector| cut -d'@' -f 1`
 
-#get input vector mapset
+# get input vector mapset
 GIS_OPT_input_mapset=`echo $GIS_OPT_vector| cut -d'@' -f 2`
 
-#read input vector categories into CAT_LIST array
+# read input vector categories into CAT_LIST array
 IFS=$'\r\n' CAT_LIST=($(cat $TMP.cat))
 
-TMP_REGION="reg`g.tempfile pid=$$`"
-#save the current region settings temporarily to avoid surpirses later.
-g.region save=$TMP_REGION
+# save the current region settings temporarily to avoid surpirses later.
+TMP_REGION="tmp_rlisetup.sampvect.$$"
+g.region save="$TMP_REGION"
 
-#process each feature in the vector having category values in the CAT_LIST array
-for CAT in "${CAT_LIST[@]}" 
+# find a free Xmonitor
+XMON=x1
+for i in 1 2 3 4 5 6 7 ; do
+   result=`d.mon -L | grep -w "^x$i"`
+   if [ `echo "$result" | grep -c 'not'` -eq 1 ] ; then
+      XMON="x$i"
+      break
+   fi
+done
+
+
+# process each feature in the vector having category values in the CAT_LIST array
+for CAT in "${CAT_LIST[@]}"
 do
-    #vector to store a feature fro $GIS_OPT_vector with category value $CAT.
-    #This temporary vector will be removed at the end. 
+    # vector to store a feature fro $GIS_OPT_vector with category value $CAT.
+    # This temporary vector will be removed at the end.
     EXTRACT=$GIS_OPT_input_vector"_"$CAT"_part@"$GIS_OPT_input_mapset
-    
-    #extract only a part of $GIS_OPT_vector where category = $CAT and store in $EXTRACT
-    v.extract input=$GIS_OPT_vector output=$EXTRACT type=point,line,boundary,centroid,area,face new=-1 -d where='CAT='$CAT
-    
-    #TODO: anyway to check if x1 is in use?
-    #opening monitor x1
-    d.mon stop=x1
-    d.mon start=x1
-    #setting region with raster resolution
-    g.region vect=$EXTRACT align=$GIS_OPT_raster
-    d.rast -o $GIS_OPT_raster    
-    #render extracted vector map
-    d.vect $EXTRACT
-    #ask the user if he wants to analyse this vector and a name for raster
-    #in graphical mode using wish
-    export name=$TMP.val # where find the answer
-    $GRASS_WISH $f_path/area_query 
-    cat $name | cut -f1 -d ' ' > $name.var
-    read ok < $name.var
-    cat $name | cut -f2 -d' ' > $name.var
-    r_name=""
-    read r_name < $name.var
-    echo $r_name
-
-    if [ $ok -eq 1 ] ; then
+
+    # extract only a part of $GIS_OPT_vector where category = $CAT and store in $EXTRACT
+    v.extract input=$GIS_OPT_vector output=$EXTRACT \
+       type=point,line,boundary,centroid,area,face \
+       new=-1 -d where='CAT='$CAT
+
+    # open Xmonitor
+    d.mon stop="$XMON"
+    d.mon start="$XMON"
+
+    # set region with raster resolution
+    g.region vect="$EXTRACT" align="$GIS_OPT_raster"
+    d.rast -o "$GIS_OPT_raster"
+
+    # render extracted vector map
+    d.vect "$EXTRACT"
+
+    # ask the user to analyse this vector and a name for raster in a Tcl GUI
+    name="$TMP.val" # where find the answer
+    export name
+
+    "$GRASS_WISH" "$f_path/area_query"
+
+    ok=`cat "$name" | cut -f1 -d ' '`
+    #cat "$name" | cut -f1 -d ' ' > "$name.var"
+    #read ok < "$name.var"
+    r_name=`cat "$name" | cut -f2 -d' '`
+    #cat "$name" | cut -f2 -d' ' > "$name.var"
+    #r_name=""
+    #read r_name < "$name.var"
+    echo "$r_name"
+
+    if [ "$ok" -eq 1 ] ; then
 	#area selected, create mask
-	v.to.rast input=$EXTRACT output=$r_name use=cat value=1 rows=4096
-	#read the region settings to save to configuration file
-	g.region -g| grep "n=" | cut -f2 -d'='> $name.var
-	read north < $name.var
-	g.region -g| grep "s=" | cut -f2 -d'='  > $name.var
-	read south < $name.var
-	g.region -g| grep "e=" | cut -f2 -d'=' > $name.var
-	read east < $name.var
-	g.region -g| grep "w=" | cut -f2 -d'=' > $name.var
-	read west < $name.var
-	#write info in configuration file
-	echo "MASKEDOVERLAYAREA $r_name|$north|$south|$east|$west" >> $GIS_OPT_conf
+	v.to.rast input="$EXTRACT" output="$r_name" use=cat value=1 rows=4096
+
+	# save the region settings into the configuration file
+	eval `g.region -g`
+	echo "MASKEDOVERLAYAREA $r_name|$n|$s|$e|$w" >> "$GIS_OPT_conf"
     fi
+
     #remove temporary vector map created from v.extract
-    g.remove vect=$EXTRACT
+    g.remove vect="$EXTRACT"
     #rm -fR "$GISDBASE"/"$LOCATION"/"$MAPSET"/vector/$GIS_OPT_vector"part"$I
-    #echo DROP TABLE $GIS_OPT_vector"part"$I | db.execute 
+    #echo DROP TABLE $GIS_OPT_vector"part"$I | db.execute
 done
-d.mon stop=x1
-#restore user region
-g.region region=$TMP_REGION
-#remove temporary region, $TMP_REGION
-g.remove region=$TMP_REGION
-# clean tmp files
-rm -f $TMP*
 
+d.mon stop="$XMON"
 
+# restore the region (which itself is a WIND_OVERRIDE temporary region by
+#  the r.li.setup main script)
+g.region region="$TMP_REGION"
+g.remove region="$TMP_REGION"
+
+# clean tmp files
+rm -f "$TMP"*

raster/r.li/r.li.setup/square_mouse_selection.sh

@@ -1,9 +1,10 @@
-#! /bin/sh 
-
+#!/bin/sh 
+#
+# This script selects a square area using the mouse
+#
 # This program is free software under the GPL (>=v2)
 # Read the COPYING file that comes with GRASS for details.
-
-#this script select a square area using mouse
+#
 
 #%Module 
 #% description: Select a rectangular area
@@ -11,80 +12,83 @@
 #%option
 #% key: raster
 #% type: string
-#% description: raster map to to analyse
+#% gisprompt: old,cell,raster
+#% description: Raster map to to analyse
 #% required: yes
 #%end
 #%option
 #% key: vector
 #% type: string
-#% description: vector to overlay
+#% gisprompt: old,vector,vector
+#% description: Vector map to overlay
 #% required: no
 #%end
 #%option
 #% key: site
 #% type: string
-#% description: site to overlay
+#% description: Vector points map to overlay
 #% required: no
 #%end
 #%option
 #% key: config
 #% type: string
-#% description: name of configuration file where insert areas
+#% gisprompt: new,file,file
+#% description: Name of configuration file where inserted areas will be stored
 #% required: yes
 #%end
 #%option
 #% key: north
 #% type: string
-#% description: nothern edge (use only with f flag)
+#% description: Northern edge (use only with the 'f' flag)
 #% required: no
 #%end
 #%option
 #% key: south
 #% type: string
-#% description:south edge (use only with f flag)
+#% description: Southern edge (use only with the 'f' flag)
 #% required: no
 #%end
 #%option
 #% key: east
 #% type: string
-#% description: east edge(use only with f flag)
+#% description: Eastern edge (use only with the 'f' flag)
 #% required: no
 #%end
 #%option
 #% key: west 
 #% type: string
-#% description: west edge(use only with f flag)
+#% description: Western edge (use only with the 'f' flag)
 #% required: no
 #%end
 #%flag
 #% key: f
-#% description: sample frame yet selected 
+#% description: Sample frame selected by module options
 #%end
 
 f_path="$GISBASE/etc/r.li.setup"
 
-# Check if we have grass
+# Check if we are in a GRASS session
 if test "$GISBASE" = ""; then
- echo "You must be in GRASS GIS to run this program." >&2
- exit 1
+   echo "You must be in GRASS GIS to run this program." >&2
+   exit 1
  fi
+
 if [ "$1" != "@ARGS_PARSED@" ] ; then
-  exec g.parser "$0" "$@"
+   exec g.parser "$0" "$@"
 fi
 
 
-
-# open x1 monitor
+# open x1 Xmonitor
 d.mon stop=x1
 d.mon start=x1
 
 
 g.region rast=$GIS_OPT_raster
 
-#### set temporary files
+#### create temporary file
 TMP="`g.tempfile pid=$$`"
 if [ $? -ne 0 ] || [ -z "$TMP" ] ; then
-    echo "ERROR: unable to create temporary files" 1>&2
+    echo "ERROR: unable to create temporary file" 1>&2
     exit 1
 fi
 
@@ -104,27 +108,33 @@ read s_ewres < $TMP.var
 echo "START $s_n|$s_s|$s_e|$s_w|$s_nsres|$s_ewres" >> $GIS_OPT_conf
 
 # show the sampling frame
-if [ $GIS_FLAG_f -eq 1 ] ; then
-    g.region n=$GIS_OPT_north s=$GIS_OPT_south e=$GIS_OPT_east w=$GIS_OPT_west
+if [ "$GIS_FLAG_f" -eq 1 ] ; then
+    g.region n="$GIS_OPT_north" s="$GIS_OPT_south" \
+	     e="$GIS_OPT_east" w="$GIS_OPT_west"
 fi
 
-d.rast -o map=$GIS_OPT_raster
+d.rast -o map="$GIS_OPT_raster"
+
 if [ -n "$GIS_OPT_vector" ] ; then
-    d.vect  map=$GIS_OPT_vector
+    d.vect map="$GIS_OPT_vector"
 fi
 if [ -n "$GIS_OPT_site" ] ; then 
-    d.vect  map=$GIS_OPT_site
+    d.vect map="$GIS_OPT_site" color=red fcolor=red size=5 icon=basic/circle
 fi
 
-#let draw area
+# let draw area
 d.zoom
 
-#ask if the selected area is right
-export name=$TMP #where write the answer
-$GRASS_WISH $f_path/square_query
-read ok < $TMP.var
-if [ $ok -eq 0 ] ; then
-    echo "NO" >> $GIS_OPT_conf
+# ask if the selected area is right
+name="$TMP"  # file where write the answer
+export name
+
+"$GRASS_WISH" "$f_path/square_query"
+
+read ok < "$TMP.var"
+
+if [ "$ok" -eq 0 ] ; then
+    echo "NO" >> "$GIS_OPT_conf"
 fi
 
 if [ $ok -eq 1 ] ; then
@@ -144,11 +154,9 @@ if [ $ok -eq 1 ] ; then
     echo "SQUAREAREA $n|$s|$e|$w|$nsres|$ewres" >> $GIS_OPT_conf
 fi
 
-#close monitor
+# close the Xmonitor
 d.mon stop=x1
+
 # clean tmp files
 rm -f $TMP*
 
-
-
-

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

@@ -16,6 +16,7 @@ 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>~/.r.li/output/</tt> folder.
+
 <p>
 If input raster is full of null values r.li.shannon returns -1. <br>
 <!-- does that mean the program exit code or raster values?? -->