scripts/create_mhd_4D.sh

   1 #!/bin/sh +x
   2
   3
   4 write_mhd_4D()
   5 {
   6   cat $orig | sed "s/NDims = .*/NDims = 4/
   7                   s/TransformMatrix = .*/TransformMatrix = 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1/
   8                   /Offset/ s/.*/& 0/
   9                   /CenterOfRotation/ s/.*/& 0/
  10                   s/AnatomicalOrientation = .*/AnatomicalOrientation = ????/
  11                   /ElementSpacing/ s/.*/& 1/
  12                   /DimSize/ s/.*/& $nbph/
  13                   s/ElementDataFile = .*/ElementDataFile = LIST/" > "$1/$file_name_4D"
  14
  15   for ph in ${listph[@]}
  16   do
  17     ph=`basename $ph`
  18     echo "$ph" >> "$1/$file_name_4D"
  19   done
  20   echo $1/$file_name_4D
  21 }
  22
  23 #################################################
  24 # create_mhd_4D         argument : repertoire   #
  25 #################################################
  26 if [ $# -lt 1 ]
  27 then
  28   echo "Usage: create_mhd_4D.sh DIRECTORY"
  29   exit 1
  30 fi
  31
  32 nb_phase_file=`find $1 -maxdepth 1 -iname "*[0-9]*.mhd" | wc -l`
  33 if [ $nb_phase_file = 0 ]
  34 then
  35   echo "No phase found in $1"
  36   exit 1
  37 fi
  38
  39
  40 list_prefix=""
  41 list_phase_file=`find $1 -maxdepth 1 -iname "*[0-9]*.mhd"`
  42 for phase_file in $list_phase_file
  43 do
  44   if grep -q "NDims = 4" $phase_file 2> /dev/null
  45   then
  46     #echo $phase_file is 4D
  47     continue;
  48   fi;
  49
  50   phase_file_name=`basename $phase_file .mhd`
  51 #   if [[ ! -z `echo "$phase_file_name" | grep "__[0-9]"` ]]
  52 #   then
  53 #     prefix=`echo $phase_file_name | sed "s/__[0-9].*/__/"`
  54 #   else
  55 #     if [[ ! -z `echo "$phase_file_name" | grep "[0-9]-.*\]"` ]]
  56 #     then
  57 #       if [[ ! -z `echo "$phase_file_name" | grep "[0-9][0-9]-.*\]"` ]]
  58 #       then
  59 #       prefix=`echo $phase_file_name | sed "s/[0-9][0-9]-.*//"`
  60 #       else
  61 #       prefix=`echo $phase_file_name | sed "s/[0-9]-.*//"`
  62 #       fi
  63 #     else
  64 #       prefix="NONE"
  65 #     fi
  66 #   fi
  67
  68   # preffix: grep sequence of characters followed by sequence of numbers and remove sequence of numbers
  69   # prefix=`echo $phase_file_name | grep -o "\(^[[:alpha:][:punct:]]*\)\([[:digit:]\.\_\-]\+\)" | sed 's/\(^[[:alpha:][:punct:]]*\)\([[:digit:]\.\_\-]\+\)/\1/'`
  70   prefix=`echo $phase_file_name | grep -o "\(^[[:alpha:][:punct:]]*\)\([[:digit:]]\+\)\([\.\_\-]*\)"`
  71   prefix=`echo $prefix | sed 's/^\-\+//' | sed 's/\(^[[:alpha:][:punct:]]*\)\([[:digit:]]\+\)\([\.\_\-]*\)/\1/'`
  72   if [[ -z $prefix ]]
  73   then
  74     prefix="NONE"
  75   fi
  76
  77   # register new preffix if not yet done
  78   if [[ -z `echo "$list_prefix" | grep -w -- "$prefix"` ]]
  79   then
  80     list_prefix="$list_prefix $prefix"
  81   fi
  82 done
  83
  84
  85 for prefix in $list_prefix
  86 do
  87   if [ "$prefix" = "NONE" ]
  88   then
  89     prefix=""
  90   fi
  91
  92   list_suffix=""
  93   list_phase_file_prefix=`find $1 -maxdepth 1 -iname "${prefix}[0-9]*.mhd"`
  94   for phase_file_prefix in $list_phase_file_prefix
  95   do
  96     if grep -q "NDims = 4" $phase_file_prefix  2> /dev/null
  97     then
  98       #echo $phase_file_prefix is 4D
  99       continue;
 100     fi;
 101     phase_file_prefix_name=`basename $phase_file_prefix .mhd`
 102 #     if [[ ! -z `echo "$phase_file_prefix_name" | grep "__[0-9]"` ]]
 103 #     then
 104 #       suffix="NONE"
 105 #     else
 106 #       if [[ ! -z `echo "$phase_file_prefix_name" | grep "[0-9]-.*\]"` ]]
 107 #       then
 108 #       suffix=`echo $phase_file_prefix_name | sed "s/.*[0-9]-//;s/_\.mhd//;s/\.mhd//"`
 109 #       else
 110 #       suffix="NONE"
 111 #       fi
 112 #     fi
 113 #
 114
 115     # suffix: grep sequence of numbers followed by sequence of characters and remove sequence of numbers
 116     # suffix=`echo $phase_file_prefix_name | grep -o "\([[:digit:]\.\_\-]\+\)\([[:alpha:][:punct:]]*$\)" | sed 's/\([[:digit:]\.\_\-]\+\)\([[:alpha:][:punct:]]*$\)/\2/'`
 117     suffix=`echo $phase_file_prefix_name | grep -o "\([\.\_\-]*\)\([[:digit:]]\+\)\([[:alpha:][:punct:]]*$\)"`
 118     if ! echo $suffix | grep -qo "^\-\+"; then
 119       suffix=`echo $suffix | sed 's/\([\.\_\-]*\)\([[:digit:]]\+\)\([[:alpha:][:punct:]]*$\)/\3/'`
 120     fi
 121     suffix=`echo $suffix | sed 's/[\.\_\-]\+$//'`
 122     if [[ -z $suffix ]]
 123     then
 124       suffix="NONE"
 125     fi
 126
 127     # register new suffix if not yet done
 128     if [[ -z `echo "$list_suffix" | grep -w -- "$suffix"` ]]
 129     then
 130       list_suffix="$list_suffix $suffix"
 131     fi
 132   done
 133
 134
 135   for suffix in $list_suffix
 136   do
 137     if [ "$suffix" = "NONE" ]
 138     then
 139       suffix=""
 140     fi
 141     orig=`find $1 -maxdepth 1 -iname "${prefix}[0-9]*${suffix}*.mhd" | grep "${prefix}[[:digit:][:punct:]]\+${suffix}[\.\_\-]*.mhd" | sort | head -n 1`
 142     listph=( `find $1 -maxdepth 1 -iname "${prefix}[0-9]*${suffix}*.*raw" | grep "${prefix}[[:digit:][:punct:]]\+${suffix}[\.\_\-]*.z*raw" | sort` )
 143     nbph=${#listph[@]}
 144
 145     # only create 4D file if potential number of phases is > 1
 146     if [ $nbph -gt 1 ]; then
 147       file_name_4D="${prefix}4D${suffix}.mhd"
 148       write_mhd_4D $1
 149     fi
 150
 151   done
 152
 153 done
 154