Merge branch 'master' of /home/dsarrut/clitk3.server

diff --git a/scripts/create_sequence.sh b/scripts/create_sequence.sh
deleted file mode 100755 (executable)
index 339d351..0000000
--- a/scripts/create_sequence.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-#Create a sequence of mhd images from the various UNTAGGED directories
-if [ $# -lt 1 ]
-then
-    echo "Usage: create_sequence.sh prefix"
-    exit 1
-fi
-for i in $1*
-do
-    filename=CT_$1_$(echo "$i" | sed "s/.*,_//;s/\..*//").mhd
-    echo $filename
-    find "$i" -iname "*.dcm" | clitkDicom2Image --focal_origin -o "$filename" --std_input
-done
-
-create_mhd_4D.sh .

diff --git a/scripts/dcm_sort_by_field.sh b/scripts/dcm_sort_by_field.sh
deleted file mode 100755 (executable)
index 81d1b6b..0000000
--- a/scripts/dcm_sort_by_field.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/bash
-if [ $# -lt 1 ]
-then
-    echo Usage: dcm_sort_by_field.sh \"field name\"
-    exit
-fi
-path_dir=`pwd`
-dir_name=`basename "$path_dir"`
-[ -d "../${dir_name}_sorted" ] && rm -r "../${dir_name}_sorted"
-mkdir "../${dir_name}_sorted"
-find . -type f -iname "*.dcm" > ../${dir_name}_sorted/dicom_files
-finished=0
-total=$(wc -l ../${dir_name}_sorted/dicom_files)
-cat ../${dir_name}_sorted/dicom_files | while :
-do
-    jobrunning=0
-    conc_jobs=50
-    while [ $jobrunning -lt $conc_jobs ]
-    do
-        read i || { wait; break 2; }
-        {
-            name="$(clitkDicomInfo "$i" | grep "$1" | head -n 1 | sed "s/.*\[//;s/.$//;s/ /_/g")"
-           [ -z "$name" ] && echo "Warning: key not found in file $i" 1>&2 && mkdir -p "../${dir_name}_unsorted" && basename=$(basename "$i") && cp -l "$i" "../${dir_name}_unsorted/$basename" && exit 1 #copy to unsorted directory if dicom key not found
-            #[ -z "$name" ] && echo "Warning: key not found in file $i" 1>&2 && exit 1 #don't do anything if dicom key not found
-            name=`echo "$name" | sed 's/\//_/g'`
-           name=`echo "$name" | sed 's/\\\/_/g'`
-           name=`echo "$name" | sed 's/\*/_/g'`
-           [ -d "../${dir_name}_sorted/$name" ] || mkdir "../${dir_name}_sorted/$name" 2>>/dev/null
-            basename=$(basename "$i")
-            cp -l "$i" "../${dir_name}_sorted/$name/$basename"
-        }&
-        jobrunning=$(( $jobrunning + 1 ))
-    done
-    finished=$(( $finished + $conc_jobs  ))
-    echo -e -n "( $finished / $total )\r"
-    wait
-done
-rm ../${dir_name}_sorted/dicom_files