vv/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 "*[0-99].[0-9].mhd" -o -iname "*[0-99]*\]*.mhd" | wc -l`
  32 nb_phase_file=`find $1 -iname "*[0-9].mhd" -o -iname "*[0-9]*\]*.mhd" | wc -l`
  33 if [ $nb_phase_file = 0 ]
  34 then
  35   echo "Error: no phase found"
  36   exit 1
  37 fi
  38
  39 ########## CT #########
  40
  41 list_pattern=""
  42 #list_phase_file=`find $1 -iname "*[0-99].[0-9].mhd"`
  43 list_phase_file=`find $1 -iname "*[0-9].mhd"`
  44 for phase_file in $list_phase_file
  45 do
  46   phase_file_name=`basename $phase_file`
  47   if [[ ! -z `echo "$phase_file_name" | grep ","` ]]
  48   then
  49     prefix=`echo $phase_file_name | sed "s/,_.*/,_/"`
  50   else
  51     prefix="NONE"
  52   fi
  53   if [[ -z `echo "$list_pattern" | grep "$prefix"` ]]
  54   then
  55     list_pattern="$list_pattern $prefix"
  56   fi
  57 done
  58
  59
  60 for pattern in $list_pattern
  61 do
  62
  63   if [ "$pattern" = "NONE" ]
  64   then
  65     pattern=""
  66   fi
  67
  68   #nbph0=`find $1 -iname "${pattern}[0-9].[0-9].mhd" | wc -l`
  69   #orig0=`find $1 -iname "${pattern}[0-9].[0-9].mhd" | sort | head -n 1`
  70   #listph0=`find $1 -iname "${pattern}[0-9].[0-9].raw" | sort`
  71
  72   #nbph1=`find $1 -iname "${pattern}[0-9][0-9].[0-9].mhd" | wc -l`
  73   #orig1=`find $1 -iname "${pattern}[0-9][0-9].[0-9].mhd" | sort | head -n 1`
  74   #listph1=`find $1 -iname "${pattern}[0-9][0-9].[0-9].raw" | sort`
  75
  76   #nbph=$(( nbph0+nbph1 ))
  77   #orig=`echo -e "$orig0\n$orig1" | head -n 1`
  78   #listph="$listph0 $listph1"
  79
  80   nbph=`find $1 -iname "${pattern}*[0-9].mhd" | wc -l`
  81   orig=`find $1 -iname "${pattern}*[0-9].mhd" | sort | head -n 1`
  82   listph=`find $1 -iname "${pattern}*[0-9].raw" | sort`
  83
  84   file_name_4D="${pattern}_4D.mhd"
  85
  86   write_mhd_4D $1
  87
  88 done
  89
  90
  91 ############ PET ###########
  92
  93 list_pattern=""
  94 #list_phase_file=`find $1 -iname "*[0-99]*\]*.mhd"`
  95 list_phase_file=`find $1 -iname "*[0-9]*\]*.mhd"`
  96 for phase_file in $list_phase_file
  97 do
  98   phase_file_name=`basename $phase_file`
  99   #if [[ ! -z `echo "$phase_file_name" | grep "[0-99]-.*\]"` ]]
 100   if [[ ! -z `echo "$phase_file_name" | grep "[0-9]-.*\]"` ]]
 101   then
 102     #prefix=`echo $phase_file_name | sed "s/.*[0-99]-/-/;s/\]_.*//"`
 103     prefix=`echo $phase_file_name | sed "s/.*[0-9]-/-/;s/\]_.*//"`
 104   else
 105     prefix="NONE"
 106   fi
 107   if [[ -z `echo "$list_pattern" | grep -- "$prefix"` ]]
 108   then
 109     list_pattern="$list_pattern $prefix"
 110   fi
 111 done
 112
 113
 114 for pattern in $list_pattern
 115 do
 116
 117   if [ "$pattern" = "NONE" ]
 118   then
 119     pattern=""
 120   fi
 121
 122   #nbph=`find $1 -iname "*[0-99]${pattern}\]*.mhd" | wc -l`
 123   #orig=`find $1 -iname "*[0-99]${pattern}\]*.mhd" | sort | head -n 1`
 124   #listph=`find $1 -iname "*[0-99]${pattern}\]*.raw" | sort`
 125
 126   nbph=`find $1 -iname "*[0-9]${pattern}\]*.mhd" | wc -l`
 127   orig=`find $1 -iname "*[0-9]${pattern}\]*.mhd" | sort | head -n 1`
 128   listph=`find $1 -iname "*[0-9]${pattern}\]*.raw" | sort`
 129
 130   #file_name_4D=`basename "$orig" | sed "s/[0-99]${pattern}\]/${pattern}\]/;s/_.mhd/_4D.mhd/"`
 131   file_name_4D=`basename "$orig" | sed "s/[0-9]${pattern}\]/${pattern}\]/;s/_.mhd/_4D.mhd/"`
 132
 133   write_mhd_4D $1
 134
 135 done