[GRASS-SVN] r62339 - grass-addons/grass7/raster/r.forestfrag
svn_grass at osgeo.org
svn_grass at osgeo.org
Wed Oct 22 02:57:31 PDT 2014
Author: neteler
Date: 2014-10-22 02:57:31 -0700 (Wed, 22 Oct 2014)
New Revision: 62339
Added:
grass-addons/grass7/raster/r.forestfrag/r.forestfrag
Removed:
grass-addons/grass7/raster/r.forestfrag/r.forestfrag.py
Modified:
grass-addons/grass7/raster/r.forestfrag/Makefile
Log:
r.forestfrag: partially revert r62338
Modified: grass-addons/grass7/raster/r.forestfrag/Makefile
===================================================================
--- grass-addons/grass7/raster/r.forestfrag/Makefile 2014-10-22 07:54:54 UTC (rev 62338)
+++ grass-addons/grass7/raster/r.forestfrag/Makefile 2014-10-22 09:57:31 UTC (rev 62339)
@@ -4,4 +4,13 @@
include $(MODULE_TOPDIR)/include/Make/Script.make
-default: script
+default: install
+
+install:
+ $(INSTALL) $(PGM) $(INST_DIR)/scripts/
+ $(INSTALL_DATA) $(HTMLDIR)/$(PGM).html $(INST_DIR)/docs/html/
+ $(INSTALL_DATA) $(ARCH_DISTDIR)/docs/man/man1/$(PGM).1 $(INST_DIR)/docs/man/man1/
+ if [ -d "$(ETC)/$(PGM)" -a "$(ls -A $(ETC)/$(PGM))" ] ; then \
+ cp -rL $(ETC)/$(PGM) $(INST_DIR)/etc/ ; \
+ fi
+
Copied: grass-addons/grass7/raster/r.forestfrag/r.forestfrag (from rev 62338, grass-addons/grass7/raster/r.forestfrag/r.forestfrag.py)
===================================================================
--- grass-addons/grass7/raster/r.forestfrag/r.forestfrag (rev 0)
+++ grass-addons/grass7/raster/r.forestfrag/r.forestfrag 2014-10-22 09:57:31 UTC (rev 62339)
@@ -0,0 +1,374 @@
+#!/bin/sh
+############################################################################
+#
+# MODULE: r.forestfrag
+#
+# AUTHOR(S): Emmanuel Sambale, Stefan Sylla, Paulo van Breugel
+#
+# PURPOSE: Creates forest fragmentation index map from a forest-/
+# non-forest raster; The index map is based on Riitters,
+# K., J. Wickham, R. O'Neill, B. Jones, and E. Smith. 2000.
+# in: Global-scale patterns of forest fragmentation.
+# Conservation Ecology 4(2): 3. [online]
+# URL:http://www.consecol.org/vol4/iss2/art3/
+#
+# NOTES This addon is an adaptation of the r.forestfrag.sh addon, to
+# work on GRASS 7.0 and to add the option to have the
+# size of the moving window determined by the user. For now
+# it does not work on GRASS 6.4. Use r.forestfrag.sh instead.
+#
+# COPYRIGHT: (C) 1997-2013 by the GRASS Development Team
+#
+# This program is free software under the GNU General Public
+# License (>=v2). Read the file COPYING that comes with GRASS
+# for details.
+#
+#############################################################################
+
+#%Module
+#% description: creates forest fragmentation index from a GRASS raster map (where forest=1, non-forest=0) based on a method developed by Riitters et. al (2000). The index is computed using a moving window of user-defined size (default=3).
+#% keywords: raster, forest, fragmentation-index, Riitters
+#%End
+
+#%Option
+#% key: input
+#% type: string
+#% gisprompt: old,cell,raster
+#% description: Name of forest raster map (where forest=1, non-forest=0)
+#% required : yes
+#%End
+
+#%option
+#% key: output
+#% type: string
+#% gisprompt: new
+#% description: Name output layer
+#% key_desc: name
+#% required: yes
+#%end
+
+#%option
+#% key: window
+#% type: integer
+#% description: Window size (odd number)
+#% key_desc: number
+#% answer : 3
+#% required: yes
+#%end
+
+#%flag
+#% key: r
+#% description: Set region to raster?
+#%end
+
+#%flag
+#% key: t
+#% description: keep temporary maps
+#%END
+
+#%flag
+#% key: s
+#% description: Run r.report on output map
+#%END
+
+#%flag
+#% key: a
+#% description: shrink the output map?
+#%END
+
+
+# For testing purposes
+#-----
+#GIS_OPT_INPUT=ForestMosaic at Testing
+#GIS_OPT_OUTPUT=FMtest
+#GIS_OPT_WINDOW=3
+#GIS_FLAG_R=0
+#GIS_FLAG_T=1
+#GIS_FLAG_S=1
+#GIS_FLAG_A=1
+#-----
+
+#=======================================================================
+## GRASS team recommandations
+#=======================================================================
+
+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 "$0" "$@"
+fi
+
+eval `g.findfile el=cell file=$GIS_OPT_INPUT`
+if [ ! "$file" ] ; then
+ echo "Raster map '$GIS_OPT_input' not found in mapset search path"
+ exit 1
+fi
+
+#=======================================================================
+## Prepare data
+#=======================================================================
+
+#set to current input map region (user option, default=current region)
+#--------------------------------------------------------------------
+if [ $GIS_FLAG_R -eq 1 ];
+then
+ echo "setting region to input map ..."
+ g.region rast=$GIS_OPT_INPUT
+fi
+
+# Set root name of temporary output files
+#--------------------------------------------------------------------
+tmpl=forestfrag$$_
+
+# get map (assuming input-map is a cell-raster with forest=1,
+# and setting all other values to 0 (assuming to be non-forest=)
+#--------------------------------------------------------------------
+g.copy rast=${GIS_OPT_INPUT},${tmpl}
+# recode forest-map: nonforest = 0, forest = 1
+r.reclass in=${tmpl} out=${tmpl}A rules=- <<EOF
+1 = 1
+* = 0
+end
+EOF
+
+#=======================================================================
+# computing pf values
+#=======================================================================
+
+echo "computing pf values ..."
+
+## let forested pixels be x and number of all pixels in moving window be y, then
+## pf=x/y"
+
+# generate grid with pixel-value=number of forest-pixels in 3x3 moving-window:
+r.neighbors input=${tmpl}A output=${tmpl}A2 method=sum size=$GIS_OPT_WINDOW
+
+# generate grid with pixel-value=number of pixels in moving window:
+r.mapcalc "${tmpl}C3 = 1.0*$GIS_OPT_WINDOW^2" --overwrite
+
+# create pf map
+r.mapcalc file=- << EOF
+${tmpl}A3 = 1.0 * ${tmpl}A2
+${tmpl}pf = (${tmpl}A3/${tmpl}C3)
+EOF
+
+#=======================================================================
+# computing pff values
+#=======================================================================
+
+echo "computing pff values ..."
+
+## Considering pairs of pixels in cardinal directions in a 3x3 window, the total
+## number of adjacent pixel pairs is 12. Assuming that x pairs include at least
+## one forested pixel, and y of those pairs are forest-forest pairs, so pff equals
+## y/x"
+
+# calculate number of 'forest-forest' pairs
+#=======================================================================
+
+echo "... calculate number of 'forest-forest' pairs"
+
+SW=$GIS_OPT_WINDOW
+tmpf=`g.tempfile pid=$$`
+echo -n "${tmpl}F1 = " >> $tmpf
+
+# Compute matrix dimensions
+SWn=$(echo "($SW - 1) / 2" | bc)
+
+# Write mapcalc expression to tmpf - rows
+rsub=$(seq $SWn -1 -$SWn)
+csub=$(seq -$SWn 1 $(echo "($SWn-1)" | bc))
+
+for k in $rsub
+do
+ for l in $csub
+ do
+ echo -n "${tmpl}A[$k,$l]*${tmpl}A[$k,$(echo "$l+1" | bc)] + " >> $tmpf
+ done
+done
+
+# Write mapcalc expression to tmpf - columns
+rsub=$(seq -$SWn 1 $SWn)
+csub=$(seq $SWn -1 $(echo "(-$SWn+1)" | bc))
+
+for k in $rsub
+do
+ for l in $csub
+ do
+ echo -n "${tmpl}A[$l,$k]*${tmpl}A[$(echo "$l-1" | bc),$k] + " >> $tmpf
+ done
+done
+
+echo -n "0" >> $tmpf
+r.mapcalc file=$tmpf
+unlink $tmpf
+
+# number of 'forest-forest' pairs
+#=======================================================================
+
+tmpf2=`g.tempfile pid=$$$$`
+echo -n "${tmpl}F2 = " >> $tmpf2
+
+# Compute matrix dimensions
+SWn=$(echo "($SW - 1) / 2" | bc)
+
+# Write mapcalc expression to tmpf - rows
+rsub=$(seq $SWn -1 -$SWn)
+csub=$(seq -$SWn 1 $(echo "($SWn-1)" | bc))
+
+for k in $rsub
+do
+ for l in $csub
+ do
+ echo -n "if((${tmpl}A[$k,$l]+${tmpl}A[$k,$(echo "$l+1" | bc)])>0,1) + " >> $tmpf2
+ done
+done
+
+# Write mapcalc expression to tmpf - columns
+rsub=$(seq -$SWn 1 $SWn)
+csub=$(seq $SWn -1 $(echo "(-$SWn+1)" | bc))
+
+for k in $rsub
+do
+ for l in $csub
+ do
+ echo -n "if((${tmpl}A[$l,$k]+${tmpl}A[$(echo "$l-1" | bc),$k])>0,1) + " >> $tmpf2
+ done
+done
+
+echo -n "0" >> $tmpf2
+r.mapcalc file=$tmpf2
+unlink $tmpf2
+
+# create pff map
+r.mapcalc --overwrite file=- << EOF
+${tmpl}F1 = 1.0 * ${tmpl}F1
+${tmpl}F2 = 1.0 * ${tmpl}F2
+${tmpl}pff = ${tmpl}F1/${tmpl}F2
+EOF
+
+#=======================================================================
+# computing fragmentation index
+#=======================================================================
+
+echo "computing fragmentation index ..."
+# (1) patch pf < 0.4
+# (2) transitional 0.4 < pf < 0.6
+# (3) edge pf > 0.6 and pf - pff < 0
+# (4) perforated pf > 0.6 and pf - pff > 0
+# (5) interior for which pf = 1.0
+# (6) undetermined pf > 0.6 and pf = pff
+
+r.mapcalc file=- << EOF
+${tmpl}pf2 = ${tmpl}pf - ${tmpl}pff
+${tmpl}f1 = if(${tmpl}pf<0.4,1,0)
+${tmpl}f2 = if(${tmpl}pf>=0.4 && ${tmpl}pf<0.6,2,0)
+${tmpl}f3 = if(${tmpl}pf>=0.6 && ${tmpl}pf2<0,3,0)
+${tmpl}f4 = if(${tmpl}pf>0.6 && ${tmpl}pf2>0,4,0)
+${tmpl}f5 = if(${tmpl}pf==1 && ${tmpl}pff==1,5,0)
+${tmpl}f6 = if(${tmpl}pf>0.6 && ${tmpl}pf<1 && ${tmpl}pf2==0,6,0)
+${tmpl}index = ${tmpl}f1+${tmpl}f2+${tmpl}f3+${tmpl}f4+${tmpl}f5+${tmpl}f6
+${tmpl}indexfin2 = ( ${tmpl}A * ${tmpl}index )
+EOF
+
+#create categories
+echo "creating colors and categories ... "
+r.reclass ${tmpl}indexfin2 out=${tmpl}indexfin3 title="frag index" rules=- <<EOF
+0 = 0 nonforest
+1 = 1 patch
+2 = 2 transitional
+3 = 3 edge
+4 = 4 perforated
+5 = 5 interior
+6 = 6 undef
+EOF
+
+
+# Shrink the region
+g.region save=rforestfrag987654321 --overwrite
+if [ $GIS_FLAG_A -eq 1 ];
+then
+ NSRES=`g.region -p -g | grep nsres= | cut -f2 -d"="`
+ EWRES=`g.region -p -g | grep ewres= | cut -f2 -d"="`
+ NSCOR=$(echo "$SW*$NSRES*0.5" | bc)
+ EWCOR=$(echo "$SW*$EWRES*0.5" | bc)
+ g.region n=n-$NSCOR s=s+$NSCOR e=e-$EWCOR w=w+$EWCOR
+fi
+
+r.mapcalc "${GIS_OPT_OUTPUT} = ${tmpl}indexfin3"
+r.null ${GIS_OPT_OUTPUT} null=0
+
+#create color codes
+r.colors ${GIS_OPT_OUTPUT} --quiet rules=- << EOF
+0 255:255:0
+1 215:48:39
+2 252:141:89
+3 254:224:139
+4 217:239:139
+5 26:152:80
+6 145:207:96
+EOF
+
+#=======================================================================
+# Clean up (user option: copy pf, pff, pf2 first)
+#=======================================================================
+
+if [ $GIS_FLAG_T -eq 1 ];
+then
+ g.copy rast=${tmpl}pf,${GIS_OPT_OUTPUT}_pf
+ g.copy rast=${tmpl}pff,${GIS_OPT_OUTPUT}_pff
+ g.copy rast=${tmpl}pf2,${GIS_OPT_OUTPUT}_pf2
+fi
+
+echo "Deleting temporary files ...."
+g.mremove -f -b --quiet rast=${tmpl}*
+
+#=======================================================================
+# computing fragmentation index
+#=======================================================================
+
+if [ $GIS_FLAG_S -eq 1 ];
+then
+
+ g.copy rast=${GIS_OPT_OUTPUT},${tmpl}_REPORT
+ # Shrink the region if output map was not trimmed
+ if [ $GIS_FLAG_A -eq 0 ];
+ then
+ NSRES=`g.region -p -g | grep nsres= | cut -f2 -d"="`
+ EWRES=`g.region -p -g | grep ewres= | cut -f2 -d"="`
+ NSCOR=$(echo "$SW*$NSRES*0.5" | bc)
+ EWCOR=$(echo "$SW*$EWRES*0.5" | bc)
+ g.region save=rforestfrag987654321
+ g.region n=n-$NSCOR s=s+$NSCOR e=e-$EWCOR w=w+$EWCOR
+ fi
+
+ echo "generate map reports ..."
+ r.report map=${tmpl}_REPORT units=h,p -n
+ echo " "
+ echo "------------------------------------------------------"
+ echo "Please note in order to avoid edge effects, the region"
+ echo "is reduced / shrinked with a number of raster cells"
+ echo "equal to 1/2 the moving window size before running"
+ echo "r.report, unless the user has already selected the "
+ echo "option to trim the output map with number of cells equal"
+ echo "to 1/2 the moving window size (default)."
+ echo "------------------------------------------------------"
+ echo " "
+fi
+
+g.remove rast=${tmpl}_REPORT --quiet
+g.region region=rforestfrag987654321
+g.remove --quiet region=rforestfrag987654321
+
+
+
+
+
+
+
+
+
+
Deleted: grass-addons/grass7/raster/r.forestfrag/r.forestfrag.py
===================================================================
--- grass-addons/grass7/raster/r.forestfrag/r.forestfrag.py 2014-10-22 07:54:54 UTC (rev 62338)
+++ grass-addons/grass7/raster/r.forestfrag/r.forestfrag.py 2014-10-22 09:57:31 UTC (rev 62339)
@@ -1,374 +0,0 @@
-#!/bin/sh
-############################################################################
-#
-# MODULE: r.forestfrag
-#
-# AUTHOR(S): Emmanuel Sambale, Stefan Sylla, Paulo van Breugel
-#
-# PURPOSE: Creates forest fragmentation index map from a forest-/
-# non-forest raster; The index map is based on Riitters,
-# K., J. Wickham, R. O'Neill, B. Jones, and E. Smith. 2000.
-# in: Global-scale patterns of forest fragmentation.
-# Conservation Ecology 4(2): 3. [online]
-# URL:http://www.consecol.org/vol4/iss2/art3/
-#
-# NOTES This addon is an adaptation of the r.forestfrag.sh addon, to
-# work on GRASS 7.0 and to add the option to have the
-# size of the moving window determined by the user. For now
-# it does not work on GRASS 6.4. Use r.forestfrag.sh instead.
-#
-# COPYRIGHT: (C) 1997-2013 by the GRASS Development Team
-#
-# This program is free software under the GNU General Public
-# License (>=v2). Read the file COPYING that comes with GRASS
-# for details.
-#
-#############################################################################
-
-#%Module
-#% description: creates forest fragmentation index from a GRASS raster map (where forest=1, non-forest=0) based on a method developed by Riitters et. al (2000). The index is computed using a moving window of user-defined size (default=3).
-#% keywords: raster, forest, fragmentation-index, Riitters
-#%End
-
-#%Option
-#% key: input
-#% type: string
-#% gisprompt: old,cell,raster
-#% description: Name of forest raster map (where forest=1, non-forest=0)
-#% required : yes
-#%End
-
-#%option
-#% key: output
-#% type: string
-#% gisprompt: new
-#% description: Name output layer
-#% key_desc: name
-#% required: yes
-#%end
-
-#%option
-#% key: window
-#% type: integer
-#% description: Window size (odd number)
-#% key_desc: number
-#% answer : 3
-#% required: yes
-#%end
-
-#%flag
-#% key: r
-#% description: Set region to raster?
-#%end
-
-#%flag
-#% key: t
-#% description: keep temporary maps
-#%END
-
-#%flag
-#% key: s
-#% description: Run r.report on output map
-#%END
-
-#%flag
-#% key: a
-#% description: shrink the output map?
-#%END
-
-
-# For testing purposes
-#-----
-#GIS_OPT_INPUT=ForestMosaic at Testing
-#GIS_OPT_OUTPUT=FMtest
-#GIS_OPT_WINDOW=3
-#GIS_FLAG_R=0
-#GIS_FLAG_T=1
-#GIS_FLAG_S=1
-#GIS_FLAG_A=1
-#-----
-
-#=======================================================================
-## GRASS team recommandations
-#=======================================================================
-
-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" "$@"
-fi
-
-eval `g.findfile el=cell file=$GIS_OPT_INPUT`
-if [ ! "$file" ] ; then
- echo "Raster map '$GIS_OPT_input' not found in mapset search path"
- exit 1
-fi
-
-#=======================================================================
-## Prepare data
-#=======================================================================
-
-#set to current input map region (user option, default=current region)
-#--------------------------------------------------------------------
-if [ $GIS_FLAG_R -eq 1 ];
-then
- echo "setting region to input map ..."
- g.region rast=$GIS_OPT_INPUT
-fi
-
-# Set root name of temporary output files
-#--------------------------------------------------------------------
-tmpl=forestfrag$$_
-
-# get map (assuming input-map is a cell-raster with forest=1,
-# and setting all other values to 0 (assuming to be non-forest=)
-#--------------------------------------------------------------------
-g.copy rast=${GIS_OPT_INPUT},${tmpl}
-# recode forest-map: nonforest = 0, forest = 1
-r.reclass in=${tmpl} out=${tmpl}A rules=- <<EOF
-1 = 1
-* = 0
-end
-EOF
-
-#=======================================================================
-# computing pf values
-#=======================================================================
-
-echo "computing pf values ..."
-
-## let forested pixels be x and number of all pixels in moving window be y, then
-## pf=x/y"
-
-# generate grid with pixel-value=number of forest-pixels in 3x3 moving-window:
-r.neighbors input=${tmpl}A output=${tmpl}A2 method=sum size=$GIS_OPT_WINDOW
-
-# generate grid with pixel-value=number of pixels in moving window:
-r.mapcalc "${tmpl}C3 = 1.0*$GIS_OPT_WINDOW^2" --overwrite
-
-# create pf map
-r.mapcalc file=- << EOF
-${tmpl}A3 = 1.0 * ${tmpl}A2
-${tmpl}pf = (${tmpl}A3/${tmpl}C3)
-EOF
-
-#=======================================================================
-# computing pff values
-#=======================================================================
-
-echo "computing pff values ..."
-
-## Considering pairs of pixels in cardinal directions in a 3x3 window, the total
-## number of adjacent pixel pairs is 12. Assuming that x pairs include at least
-## one forested pixel, and y of those pairs are forest-forest pairs, so pff equals
-## y/x"
-
-# calculate number of 'forest-forest' pairs
-#=======================================================================
-
-echo "... calculate number of 'forest-forest' pairs"
-
-SW=$GIS_OPT_WINDOW
-tmpf=`g.tempfile pid=$$`
-echo -n "${tmpl}F1 = " >> $tmpf
-
-# Compute matrix dimensions
-SWn=$(echo "($SW - 1) / 2" | bc)
-
-# Write mapcalc expression to tmpf - rows
-rsub=$(seq $SWn -1 -$SWn)
-csub=$(seq -$SWn 1 $(echo "($SWn-1)" | bc))
-
-for k in $rsub
-do
- for l in $csub
- do
- echo -n "${tmpl}A[$k,$l]*${tmpl}A[$k,$(echo "$l+1" | bc)] + " >> $tmpf
- done
-done
-
-# Write mapcalc expression to tmpf - columns
-rsub=$(seq -$SWn 1 $SWn)
-csub=$(seq $SWn -1 $(echo "(-$SWn+1)" | bc))
-
-for k in $rsub
-do
- for l in $csub
- do
- echo -n "${tmpl}A[$l,$k]*${tmpl}A[$(echo "$l-1" | bc),$k] + " >> $tmpf
- done
-done
-
-echo -n "0" >> $tmpf
-r.mapcalc file=$tmpf
-unlink $tmpf
-
-# number of 'forest-forest' pairs
-#=======================================================================
-
-tmpf2=`g.tempfile pid=$$$$`
-echo -n "${tmpl}F2 = " >> $tmpf2
-
-# Compute matrix dimensions
-SWn=$(echo "($SW - 1) / 2" | bc)
-
-# Write mapcalc expression to tmpf - rows
-rsub=$(seq $SWn -1 -$SWn)
-csub=$(seq -$SWn 1 $(echo "($SWn-1)" | bc))
-
-for k in $rsub
-do
- for l in $csub
- do
- echo -n "if((${tmpl}A[$k,$l]+${tmpl}A[$k,$(echo "$l+1" | bc)])>0,1) + " >> $tmpf2
- done
-done
-
-# Write mapcalc expression to tmpf - columns
-rsub=$(seq -$SWn 1 $SWn)
-csub=$(seq $SWn -1 $(echo "(-$SWn+1)" | bc))
-
-for k in $rsub
-do
- for l in $csub
- do
- echo -n "if((${tmpl}A[$l,$k]+${tmpl}A[$(echo "$l-1" | bc),$k])>0,1) + " >> $tmpf2
- done
-done
-
-echo -n "0" >> $tmpf2
-r.mapcalc file=$tmpf2
-unlink $tmpf2
-
-# create pff map
-r.mapcalc --overwrite file=- << EOF
-${tmpl}F1 = 1.0 * ${tmpl}F1
-${tmpl}F2 = 1.0 * ${tmpl}F2
-${tmpl}pff = ${tmpl}F1/${tmpl}F2
-EOF
-
-#=======================================================================
-# computing fragmentation index
-#=======================================================================
-
-echo "computing fragmentation index ..."
-# (1) patch pf < 0.4
-# (2) transitional 0.4 < pf < 0.6
-# (3) edge pf > 0.6 and pf - pff < 0
-# (4) perforated pf > 0.6 and pf - pff > 0
-# (5) interior for which pf = 1.0
-# (6) undetermined pf > 0.6 and pf = pff
-
-r.mapcalc file=- << EOF
-${tmpl}pf2 = ${tmpl}pf - ${tmpl}pff
-${tmpl}f1 = if(${tmpl}pf<0.4,1,0)
-${tmpl}f2 = if(${tmpl}pf>=0.4 && ${tmpl}pf<0.6,2,0)
-${tmpl}f3 = if(${tmpl}pf>=0.6 && ${tmpl}pf2<0,3,0)
-${tmpl}f4 = if(${tmpl}pf>0.6 && ${tmpl}pf2>0,4,0)
-${tmpl}f5 = if(${tmpl}pf==1 && ${tmpl}pff==1,5,0)
-${tmpl}f6 = if(${tmpl}pf>0.6 && ${tmpl}pf<1 && ${tmpl}pf2==0,6,0)
-${tmpl}index = ${tmpl}f1+${tmpl}f2+${tmpl}f3+${tmpl}f4+${tmpl}f5+${tmpl}f6
-${tmpl}indexfin2 = ( ${tmpl}A * ${tmpl}index )
-EOF
-
-#create categories
-echo "creating colors and categories ... "
-r.reclass ${tmpl}indexfin2 out=${tmpl}indexfin3 title="frag index" rules=- <<EOF
-0 = 0 nonforest
-1 = 1 patch
-2 = 2 transitional
-3 = 3 edge
-4 = 4 perforated
-5 = 5 interior
-6 = 6 undef
-EOF
-
-
-# Shrink the region
-g.region save=rforestfrag987654321 --overwrite
-if [ $GIS_FLAG_A -eq 1 ];
-then
- NSRES=`g.region -p -g | grep nsres= | cut -f2 -d"="`
- EWRES=`g.region -p -g | grep ewres= | cut -f2 -d"="`
- NSCOR=$(echo "$SW*$NSRES*0.5" | bc)
- EWCOR=$(echo "$SW*$EWRES*0.5" | bc)
- g.region n=n-$NSCOR s=s+$NSCOR e=e-$EWCOR w=w+$EWCOR
-fi
-
-r.mapcalc "${GIS_OPT_OUTPUT} = ${tmpl}indexfin3"
-r.null ${GIS_OPT_OUTPUT} null=0
-
-#create color codes
-r.colors ${GIS_OPT_OUTPUT} --quiet rules=- << EOF
-0 255:255:0
-1 215:48:39
-2 252:141:89
-3 254:224:139
-4 217:239:139
-5 26:152:80
-6 145:207:96
-EOF
-
-#=======================================================================
-# Clean up (user option: copy pf, pff, pf2 first)
-#=======================================================================
-
-if [ $GIS_FLAG_T -eq 1 ];
-then
- g.copy rast=${tmpl}pf,${GIS_OPT_OUTPUT}_pf
- g.copy rast=${tmpl}pff,${GIS_OPT_OUTPUT}_pff
- g.copy rast=${tmpl}pf2,${GIS_OPT_OUTPUT}_pf2
-fi
-
-echo "Deleting temporary files ...."
-g.mremove -f -b --quiet rast=${tmpl}*
-
-#=======================================================================
-# computing fragmentation index
-#=======================================================================
-
-if [ $GIS_FLAG_S -eq 1 ];
-then
-
- g.copy rast=${GIS_OPT_OUTPUT},${tmpl}_REPORT
- # Shrink the region if output map was not trimmed
- if [ $GIS_FLAG_A -eq 0 ];
- then
- NSRES=`g.region -p -g | grep nsres= | cut -f2 -d"="`
- EWRES=`g.region -p -g | grep ewres= | cut -f2 -d"="`
- NSCOR=$(echo "$SW*$NSRES*0.5" | bc)
- EWCOR=$(echo "$SW*$EWRES*0.5" | bc)
- g.region save=rforestfrag987654321
- g.region n=n-$NSCOR s=s+$NSCOR e=e-$EWCOR w=w+$EWCOR
- fi
-
- echo "generate map reports ..."
- r.report map=${tmpl}_REPORT units=h,p -n
- echo " "
- echo "------------------------------------------------------"
- echo "Please note in order to avoid edge effects, the region"
- echo "is reduced / shrinked with a number of raster cells"
- echo "equal to 1/2 the moving window size before running"
- echo "r.report, unless the user has already selected the "
- echo "option to trim the output map with number of cells equal"
- echo "to 1/2 the moving window size (default)."
- echo "------------------------------------------------------"
- echo " "
-fi
-
-g.remove rast=${tmpl}_REPORT --quiet
-g.region region=rforestfrag987654321
-g.remove --quiet region=rforestfrag987654321
-
-
-
-
-
-
-
-
-
-
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