scripts/create_mhd_4D.sh

   1 #!/bin/sh
   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 }
  21
  22 #################################################
  23 # create_mhd_4D         argument : repertoire   #
  24 #################################################
  25 if [ $# -lt 1 ]
  26 then
  27   echo "Usage: create_mhd_4D.sh DIRECTORY"
  28   exit 1
  29 fi
  30
  31 nb_phase_file=`find $1 -iname "*[0-9]*.mhd" -o -iname "*[0-9]*\]*.mhd" | wc -l`
  32 if [ $nb_phase_file = 0 ]
  33 then
  34   echo "Error: no phase found"
  35   exit 1
  36 fi
  37
  38 ########## CT #########
  39
  40 list_pattern=""
  41 list_phase_file=`find $1 -iname "*[0-9]*.mhd"`
  42 for phase_file in $list_phase_file
  43 do
  44   phase_file_name=`basename $phase_file`
  45   if [[ ! -z `echo "$phase_file_name" | grep ","` ]]
  46   then
  47     prefix=`echo $phase_file_name | sed "s/,_.*/,_/"`
  48   else
  49     prefix="NONE"
  50   fi
  51   if [[ -z `echo "$list_pattern" | grep "$prefix"` ]]
  52   then
  53     list_pattern="$list_pattern $prefix"
  54   fi
  55 done
  56
  57
  58 for pattern in $list_pattern
  59 do
  60
  61   if [ "$pattern" = "NONE" ]
  62   then
  63     pattern=""
  64   fi
  65
  66   nbph=`find $1 -iname "${pattern}*[0-9]*.mhd" | wc -l`
  67   orig=`find $1 -iname "${pattern}*[0-9]*.mhd" | sort | head -n 1`
  68   listph=`find $1 -iname "${pattern}*[0-9]*.raw" | sort`
  69
  70   file_name_4D="${pattern}_4D.mhd"
  71   echo $file_name_4D
  72
  73   write_mhd_4D $1
  74
  75 done
  76
  77
  78 ############ PET ###########
  79
  80 list_pattern=""
  81 list_phase_file=`find $1 -iname "*[0-9]*\]*.mhd"`
  82 for phase_file in $list_phase_file
  83 do
  84   phase_file_name=`basename $phase_file`
  85   if [[ ! -z `echo "$phase_file_name" | grep "[0-9]-.*\]"` ]]
  86   then
  87     prefix=`echo $phase_file_name | sed "s/.*[0-9]-/-/;s/\]_.*//"`
  88   else
  89     prefix="NONE"
  90   fi
  91   if [[ -z `echo "$list_pattern" | grep -- "$prefix"` ]]
  92   then
  93     list_pattern="$list_pattern $prefix"
  94   fi
  95 done
  96
  97
  98 for pattern in $list_pattern
  99 do
 100
 101   if [ "$pattern" = "NONE" ]
 102   then
 103     pattern=""
 104   fi
 105
 106   nbph=`find $1 -iname "*[0-9]${pattern}\]*.mhd" | wc -l`
 107   orig=`find $1 -iname "*[0-9]${pattern}\]*.mhd" | sort | head -n 1`
 108   listph=`find $1 -iname "*[0-9]${pattern}\]*.raw" | sort`
 109
 110   file_name_4D=`basename "$orig" | sed "s/[0-9]${pattern}\]/${pattern}\]/;s/_.mhd/_4D.mhd/"`
 111
 112   write_mhd_4D $1
 113
 114 done