+#! /bin/sh +x
+
+###############################################################################
+#
+# FILE: common.sh
+# AUTHOR: RĂ´mulo Pinho 05/08/2011
+#
+# Helper file with many functions used in the midP scripts.
+#
+###############################################################################
+
+
+# block execution untill the number of threads (jobs) launched by the
+# current process is below the given number of threads.
+MAX_THREADS=2
+check_threads()
+{
+ nbth=$1
+ while [[ $(jobs -p | wc -l) -ge $nbth ]]; do
+ jobs
+ sleep 10
+ done
+}
+
+#
+# receive a 4D file and and extract the corresponding phase numbers
+# export the variables containing each of the extracted data
+#
+extract_4d_phase_numbers()
+{
+ mhd4d=$1
+
+ nb_phases=${#phase_files[@]}
+
+ # get everything except numbers and punctuation
+ cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "[^0-9[:punct:]]*" | sort -u > /tmp/patterns.txt
+
+ # find which patterns have the phases connected to it
+ patterns=`cat /tmp/patterns.txt`
+ if [ -z "$patterns" ]; then
+ phase_nbs=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep "[0-9]\+"` )
+ else
+ for i in $patterns; do
+
+ # check if the pattern appears before the phase number
+ nb_phases_found=`cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "$i[0-9[:punct:]]\+" | sort -u | wc -l`
+ if [ $nb_phases_found == $nb_phases ]; then
+ # keep only what identifies the phase number
+ phase_nbs=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "$i[0-9[:punct:]]\+" | grep -o "[^${i}]\+" | grep -o "[0-9]\+[[:punct:]]*[0-9]*" | grep -o "[0-9]*[[:punct:]]*[0-9]\+"` )
+ break
+ fi
+
+ # check if the pattern appears after the phase number
+ nb_phases_found=`cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$i" | sort -u | wc -l`
+ if [ $nb_phases_found == $nb_phases ]; then
+ # keep only what identifies the phase number
+ phase_nbs=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | sed 's/.mhd//' | grep -o "[0-9[:punct:]]\+$i" | grep -o "[^${i}]\+" | grep -o "[0-9]\+[[:punct:]]*[0-9]*" | grep -o "[0-9]*[[:punct:]]*[0-9]\+"` )
+ break
+ fi
+
+ done
+ fi
+
+ echo "Phase numbers are ${phase_nbs[@]}"
+ rm /tmp/patterns.txt
+}
+
+#
+# receive a 4D file and extract the corresponding phase files,
+# and phase numbers.
+# export the variables containing each of the extracted data
+#
+extract_4d_phases()
+{
+ mhd4d=$1
+
+ echo "4D file is $mhd4d"
+
+ # array of phase files
+ phase_files=( `cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:'` )
+ echo "Phase files are ${phase_files[@]}"
+
+ extract_4d_phase_numbers $mhd4d
+}
+
+
+#
+# receive a 4D file and the reference phase number as input
+# and extract the corresponding phase files, phase numbers,
+# and reference phase file.
+#
+# export the variables containing each of the extracted data
+#
+extract_4d_phases_ref()
+{
+ extract_4d_phases $1
+
+ # reference phase file
+ ref_phase_file=`cat $mhd4d | grep ".raw" | sed 's:.raw:.mhd:' | grep $2`
+ echo "Reference phase is $ref_phase_file"
+
+ # reference phase number
+ for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
+ ref_phase_nb=`echo ${phase_nbs[$i]} | grep $2`
+ if [ -n "$ref_phase_nb" ]; then
+ echo "Reference phase number is $ref_phase_nb"
+ break
+ fi
+ done
+}