ndmanage-plugins_bsd.patch

diff -ur scripts/duration scripts/duration
--- scripts/duration 2012-03-19 19:08:42.000000000 +0100
+++ scripts/duration	2012-12-19 15:30:29.000000000 +0100
@@ -14,24 +14,24 @@
 #//
 #////////////////////////////////////////////////////////////////////////////
 
-BLACK="\e[1;30m"
-DARK_GREY="\e[1;30m"
-BLUE="\e[1;34m"
-LIGHT_BLUE="\e[1;34m"
-GREEN="\e[0;32m"
-LIGHT_GREEN="\e[1;32m"
-CYAN="\e[1;36m"
-LIGHT_CYAN="\e[1;36m"
-RED="\e[1;31m"
-LIGHT_RED="\e[1;31m"
-PURPLE="\e[0;35m"
-LIGHT_PURPLE="\e[1;35m"
-BROWN="\e[0;33m"
-YELLOW="\e[1;33m"
-LIGHT_GREY="\e[1;37m"
-WHITE="\e[1;37m"
-BOLD_BLACK="\e[1m"
-PLAIN="\e[0m"
+BLACK="\x1B[1;30m"
+DARK_GREY="\x1B[1;30m"
+BLUE="\x1B[1;34m"
+LIGHT_BLUE="\x1B[1;34m"
+GREEN="\x1B[0;32m"
+LIGHT_GREEN="\x1B[1;32m"
+CYAN="\x1B[1;36m"
+LIGHT_CYAN="\x1B[1;36m"
+RED="\x1B[1;31m"
+LIGHT_RED="\x1B[1;31m"
+PURPLE="\x1B[0;35m"
+LIGHT_PURPLE="\x1B[1;35m"
+BROWN="\x1B[0;33m"
+YELLOW="\x1B[1;33m"
+LIGHT_GREY="\x1B[1;37m"
+WHITE="\x1B[1;37m"
+BOLD_BLACK="\x1B[1m"
+PLAIN="\x1B[0m"
 
 #////////////////////////////////////////////////////////////////////////////
 #//   Compute and print duration
diff -ur scripts/ndm_functions scripts/ndm_functions
--- scripts/ndm_functions	2011-12-06 17:20:31.000000000 +0100
+++ scripts/ndm_functions	2012-12-19 15:30:29.000000000 +0100
@@ -52,24 +52,24 @@
 INPUTS_MISSING=11
 VAR_MISSING=20
 
-BLACK="\e[1;30m"
-DARK_GREY="\e[1;30m"
-BLUE="\e[1;34m"
-LIGHT_BLUE="\e[1;34m"
-GREEN="\e[1;32m"
-LIGHT_GREEN="\e[1;32m"
-CYAN="\e[1;36m"
-LIGHT_CYAN="\e[1;36m"
-RED="\e[1;31m"
-LIGHT_RED="\e[1;31m"
-PURPLE="\e[1;35m"
-LIGHT_PURPLE="\e[1;35m"
-BROWN="\e[0;33m"
-YELLOW="\e[1;33m"
-LIGHT_GREY="\e[1;37m"
-WHITE="\e[1;37m"
-BOLD_BLACK="\e[1m"
-PLAIN="\e[0m"
+BLACK="\x1B[1;30m"
+DARK_GREY="\x1B[1;30m"
+BLUE="\x1B[1;34m"
+LIGHT_BLUE="\x1B[1;34m"
+GREEN="\x1B[1;32m"
+LIGHT_GREEN="\x1B[1;32m"
+CYAN="\x1B[1;36m"
+LIGHT_CYAN="\x1B[1;36m"
+RED="\x1B[1;31m"
+LIGHT_RED="\x1B[1;31m"
+PURPLE="\x1B[1;35m"
+LIGHT_PURPLE="\x1B[1;35m"
+BROWN="\x1B[0;33m"
+YELLOW="\x1B[1;33m"
+LIGHT_GREY="\x1B[1;37m"
+WHITE="\x1B[1;37m"
+BOLD_BLACK="\x1B[1m"
+PLAIN="\x1B[0m"
 
 #////////////////////////////////////////////////////////////////////////////
 #//  Messages (erros, warnings, headers)

diff -ur scripts/duration scripts/duration
--- scripts/duration 2012-03-19 19:08:42.000000000 +0100
+++ scripts/duration	2012-12-19 14:47:28.000000000 +0100
@@ -137,7 +137,7 @@
 	# 5) start with one or more chars, then '.', then three chars, then one or more chars (for 'evt' etc.)
 	case5='/^.+\.[^.]{3}\.([^.-]*)+(-shifted)?$/'
 
-	extension=$(basename $filename | sed -r -e "$case1 s//\1/;$case2 s//\1/;$case3 s//\1/;$case4 s//\1/;$case5 s//\1/")
+	extension=$(basename $filename | sed -E -e "$case1 s//\1/;$case2 s//\1/;$case3 s//\1/;$case4 s//\1/;$case5 s//\1/")
 
 	# Compute duration in ms
 	case $extension in
diff -ur scripts/ndm_functions scripts/ndm_functions
--- scripts/ndm_functions	2011-12-06 17:20:31.000000000 +0100
+++ scripts/ndm_functions	2012-12-19 14:47:28.000000000 +0100
@@ -78,7 +78,7 @@
 # Print error message
 echo_error()
 {
-	indent=$(echo "$1"|sed -r 's/^([ ]*).*/\1/')
+	indent=$(echo "$1"|sed -E 's/^([ ]*).*/\1/')
 	message=$(echo "$1"|sed 's/^ *//g')
 
 	echo -en "$RED" >&2
@@ -89,7 +89,7 @@
 # Print warning message
 echo_warning()
 {
-	indent=$(echo "$1"|sed -r 's/^([ ]*).*/\1/')
+	indent=$(echo "$1"|sed -E 's/^([ ]*).*/\1/')
 	message=$(echo "$1"|sed 's/^ *//g')
 
 	echo -en "$BLUE" >&2
@@ -111,7 +111,7 @@
 # 			break
 # 		fi
 # 	done
-# 	indent=$(echo "$1"|sed -r 's/^([ ]*).*/\1/')
+# 	indent=$(echo "$1"|sed -E 's/^([ ]*).*/\1/')
 # 	message=$(echo "$1"|sed 's/^ *//g')
 #
 	echo $*
@@ -469,13 +469,13 @@
 	# Start with the 'easy' ones
 	date=$(filename_date $dirname)
 	[ -z "$date" ] && return
-	prefix=$(echo $dirname|sed -r '/(.*)-'$date'.*/!d;s//\1/')
+	prefix=$(echo $dirname|sed -E '/(.*)-'$date'.*/!d;s//\1/')
 
 	# Deal with the 'hard' end of the filename
 	description=${dirname#$prefix-$date}
 	if [ -z "$suffix" ] && ! $no_suffix
 	then
-		suffix=$(echo $description|sed -r '/.*-(.*)/!d;s//\1/')
+		suffix=$(echo $description|sed -E '/.*-(.*)/!d;s//\1/')
 	fi
 	description=${description%$suffix}
 	description=${description%-}
@@ -535,26 +535,26 @@
 	# Start with the 'easy' ones
 	date=$(filename_date $filename)
 	[ -z "$date" ] && return
-	prefix=$(echo $filename|sed -r '/(.*)-'$date'.*/!d;s//\1/')
-	nn=$(echo $filename|sed -r '/'$prefix'-'$date'-([0-9]{2})-.*/!d;s//\1/')
-	extension=$(echo $filename|sed -r '/.*[.](.*)/!d;s//\1/')
+	prefix=$(echo $filename|sed -E '/(.*)-'$date'.*/!d;s//\1/')
+	nn=$(echo $filename|sed -E '/'$prefix'-'$date'-([0-9]{2})-.*/!d;s//\1/')
+	extension=$(echo $filename|sed -E '/.*[.](.*)/!d;s//\1/')
 	[ ! -z "$extension" ] && p_extension=.$extension
 
 	# Special case: evt files end in .ccc.evt where 'c' is any character
 	if [ "$extension" == "evt" ]
 	then
-		evt=$(echo $filename|sed -r '/.*[.](.{3})[.]'$extension'/!d;s//\1/')
+		evt=$(echo $filename|sed -E '/.*[.](.{3})[.]'$extension'/!d;s//\1/')
 		[ ! -z "$evt" ] && p_evt=.$evt
 	fi
 
 	# Deal with the 'hard' end of the filename
-	end=$(echo $filename|sed -r '/'$prefix'-'$date'-'$nn'-(.*)'$p_evt$p_extension'/!d;s//\1/')
-	NNN=$(echo $end|sed -r '/.*-([0-9]+).*/!d;s//\1/')
+	end=$(echo $filename|sed -E '/'$prefix'-'$date'-'$nn'-(.*)'$p_evt$p_extension'/!d;s//\1/')
+	NNN=$(echo $end|sed -E '/.*-([0-9]+).*/!d;s//\1/')
 	description=${end%-$NNN}
 	description=${description%$p_evt}
 	if [ -z "$suffix" ] && ! $no_suffix
 	then
-		suffix=$(echo $description|sed -r '/.*-(.*)/!d;s//\1/')
+		suffix=$(echo $description|sed -E '/.*-(.*)/!d;s//\1/')
 	fi
 	description=${description%-$suffix}
 
@@ -585,9 +585,9 @@
 	local filename=$1
 
 	# Case 1: date is specified as YYYYMMDD in the file name
-	d=$(echo $filename | sed -r '/.*([0-9]{8}).*/!d;s//\1/')
+	d=$(echo $filename | sed -E '/.*([0-9]{8}).*/!d;s//\1/')
 	# Case 2: date is specified as YYYY-MM-DD in the file name
-	[ -z "$d" ] && d=$(echo $filename | sed -r '/.*([0-9]{4}-[0-9]{2}-[0-9]{2}).*/!d; s//\1/')
+	[ -z "$d" ] && d=$(echo $filename | sed -E '/.*([0-9]{4}-[0-9]{2}-[0-9]{2}).*/!d; s//\1/')
 
 	echo $d
 }
@@ -601,9 +601,9 @@
 	local d
 
 	# Case 1: date is specified as YYYYMMDD in the file name
-	d=$(echo $1 | sed -r '/.*([0-9]{4})([0-9]{2})([0-9]{2}).*/!d;s//\1-\2-\3/')
+	d=$(echo $1 | sed -E '/.*([0-9]{4})([0-9]{2})([0-9]{2}).*/!d;s//\1-\2-\3/')
 	# Case 2: date is specified as YYYY-MM-DD in the file name
-	[ -z "$d" ] && d=$(echo $1 | sed -r '/.*([0-9]{4}-[0-9]{2}-[0-9]{2}).*/!d; s//\1/')
+	[ -z "$d" ] && d=$(echo $1 | sed -E '/.*([0-9]{4}-[0-9]{2}-[0-9]{2}).*/!d; s//\1/')
 
 	echo $d
 }
@@ -705,7 +705,7 @@
 	for (( i=0;i<$n;i++ ))
 	do
 		suffix=$(get_suffix $i ${suffixes[*]})
-		file_list="$file_list $(ls ../$directory-$suffix|cut -d/ -f 3|sed -r 's/(.*)-'$suffix'.*/\1/g')"
+		file_list="$file_list $(ls ../$directory-$suffix|cut -d/ -f 3|sed -E 's/(.*)-'$suffix'.*/\1/g')"
 	done
 
 	# List all sessions
diff -ur scripts/ndm_recolorchannels scripts/ndm_recolorchannels
--- scripts/ndm_recolorchannels	2010-04-15 11:29:14.000000000 +0200
+++ scripts/ndm_recolorchannels	2012-12-19 14:54:28.000000000 +0100
@@ -77,4 +77,4 @@
 	command='/'$s'/N;/'$s'/N;/'$s'/s/#....../#'${color[$i]}'/g;'$command
 done
 
-[ ! -z "$command" ] && sed -i -e $command $file
+[ ! -z "$command" ] && sed -i '' -e $command $file
diff -ur scripts/ndm_start scripts/ndm_start
--- scripts/ndm_start	2012-09-26 17:11:02.000000000 +0200
+++ scripts/ndm_start	2012-12-19 14:54:28.000000000 +0100
@@ -267,7 +267,7 @@
 		then
 			echo_warning "directory name '$directory' does not seem to contain a date"
 		else
-			sed -i 's/<date>.*<\/date>/<date>'$d'<\/date>/' $template.xml
+			sed -i '' 's/<date>.*<\/date>/<date>'$d'<\/date>/' $template.xml
 		fi
 		if [ -f $directory.xml ] && ! diff -I '<date>' -q $template.xml $directory.xml >/dev/null
 		then
diff -ur scripts/process_renameevents_SPWR scripts/process_renameevents_SPWR
--- scripts/process_renameevents_SPWR	2011-01-29 00:13:40.000000000 +0100
+++ scripts/process_renameevents_SPWR	2012-12-19 14:54:28.000000000 +0100
@@ -30,7 +30,7 @@
 [ -z "$(ls $session*evt 2> /dev/null)" ] && exit $NO_ERROR
 for eventfile in $session*evt
 do
-	sed -i \
+	sed -i '' \
 		-e 's/[[:space:]]0$/\tStimulation/' \
 		-e 's/[[:space:]]1$/\tRipple Left/' \
 		-e 's/[[:space:]]2$/\tRipple Right/' \
diff -ur scripts/process_renameevents_TMaze scripts/process_renameevents_TMaze
--- scripts/process_renameevents_TMaze	2011-01-29 00:13:27.000000000 +0100
+++ scripts/process_renameevents_TMaze	2012-12-19 14:54:28.000000000 +0100
@@ -27,7 +27,7 @@
 [ -z "$(ls $session*evt 2> /dev/null)" ] && exit $NO_ERROR
 for eventfile in $session*evt
 do
-	sed -i \
+	sed -i '' \
 		-e 's/[[:space:]]0$/\tTurn left/' \
 		-e 's/[[:space:]]1$/\tTurn right/' \
 		-e 's/[[:space:]]100$/\tTrial start/' \

--- src/process_extractspikes/process_extractspikes.cpp.orig 2012-08-17 20:36:21.000000000 +0200
+++ src/process_extractspikes/process_extractspikes.cpp	2012-08-17 20:37:31.000000000 +0200
@@ -1616,7 +1616,7 @@
 	char *groups, *currentGroup, *thresholds; // Groups of electrodes and thr
 
 	// extract thresholds from arguments
-	groups = strdupa (arguments.thresList); // Split groups
+	groups = strdup (arguments.thresList); // Split groups
 	currentGroup = strsep (&groups, GROUP_SEPARATOR); // focus on the 1st group
 
 	while(currentGroup != NULL) {
@@ -1665,7 +1665,7 @@
 	char *groups, *currentGroup, *channels; // Groups of electrodes and channels
 
 	// extract channels from arguments
-	groups = strdupa (arguments.channelList); // Split groups
+	groups = strdup (arguments.channelList); // Split groups
 	currentGroup = strsep (&groups, GROUP_SEPARATOR); // focus on the 1st group
 
 	while(currentGroup != NULL) {

--- src/process_medianthreshold/process_medianthreshold.cpp.orog 2012-08-17 20:39:55.000000000 +0200
+++ src/process_medianthreshold/process_medianthreshold.cpp	2012-08-17 20:40:06.000000000 +0200
@@ -193,7 +193,7 @@
 	} // for i
 
 	/** Computes threshold for each channel groups */
-	groups = strdupa (arguments.channelList); // Split groups
+	groups = strdup (arguments.channelList); // Split groups
 	currentGroup = strsep (&groups, GROUP_SEPARATOR); // focus on the first group
 
 	while(currentGroup != NULL) {