new midP related scripts

[clitk.git] / scripts / common.sh

diff --git a/scripts/common.sh b/scripts/common.sh
index e06bf255d1e9b8caa06148bb2b0b42f724845a21..73d17873c7bc30135074e130c1767b027d22e4bc 100755 (executable)
--- a/scripts/common.sh
+++ b/scripts/common.sh
@@ -1,14 +1,110 @@
-#! /bin/sh
+#! /bin/sh +x
 
+###############################################################################
+#
+# FILE: common.sh
+# AUTHOR: Rômulo Pinho 05/08/2011
+#
+# Helper file with many functions used in the midP scripts.
+#
+###############################################################################
 
-MAX_THREADS=2
 
+# 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()
 {
-    while [[ $(jobs -p | wc -l) -ge $1 ]]; do
-        jobs
-        sleep 10
+  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
+}