[clitk-commits-list] Clitk branch master updated. v1.2.0-611-gcdec3fe
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http://git.creatis.insa-lyon.fr/pubgit/?p=clitk.git;a=commitdiff;h=cdec3fe358bfd005cb60ad6bf83def00291c86ea
commit cdec3fe358bfd005cb60ad6bf83def00291c86ea
Author: Romulo Pinho <romulo.pinho at lyon.unicancer.fr>
Date: Thu Dec 22 17:50:48 2011 +0100
midpP: combine VF's after inverting and composing
diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh
index 3cd023c..c38555a 100755
--- a/scripts/create_midP-2.0.sh
+++ b/scripts/create_midP-2.0.sh
@@ -221,6 +221,107 @@ midp()
echo
}
+midp_in_out()
+{
+ echo
+ echo "----------- Mid-position ------------"
+ start=`date`
+ echo "start: $start"
+ echo
+
+ mkdir -p $midp_dir
+
+ ########### calculate the midp wrt the reference phase
+ phase_nb=$ref_phase_nb
+ phase_file=$ref_phase_file
+ echo "Calculating midp_$phase_nb.mhd..."
+ vf_midp_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
+ vf_midp_out=$midp_dir/vf_outside_midp_$phase_nb.mhd
+ # average the vf's from reference phase to phase
+ clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
+ abort_on_error midp $? clean_up_midp
+ clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
+ abort_on_error midp $? clean_up_midp
+
+ # invert the vf (why?)
+ clitkInvertVF -i $vf_midp_in -o $vf_midp_in
+ abort_on_error midp $? clean_up_midp
+ clitkInvertVF -i $vf_midp_out -o $vf_midp_out
+ abort_on_error midp $? clean_up_midp
+
+ # combine in and out VF's
+ ref_vf_midp_in=$vf_midp_in
+ ref_vf_midp_out=$vf_midp_out
+ vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
+ clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
+ clitkZeroVF -i $vf_midp -o vf_zero.mhd
+ clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
+
+ # create the midp by warping the reference phase with the reference vf
+ midp=$midp_dir/midp_$phase_nb.mhd
+ clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
+ abort_on_error midp $? clean_up_midp
+
+ clitkImageConvert -i $midp -o $midp -t float
+ abort_on_error midp $? clean_up_midp
+
+ ########### calculate the midp wrt the other phases
+ for i in $( seq 0 $((${#phase_files[@]} - 1))); do
+ phase_file=${phase_files[$i]}
+ phase_nb=${phase_nbs[$i]}
+ vf_midp_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
+ vf_midp_out=$midp_dir/vf_outside_midp_$phase_nb.mhd
+
+ if [ "$phase_nb" != "$ref_phase_nb" ]; then
+ echo "Calculating midp_$phase_nb.mhd..."
+ # calculate vf from phase to midp, using the vf from reference phase to midp (-i)
+ # and the vf from reference phase to phase (-j)
+ clitkComposeVF -i $ref_vf_midp_in -j $vf_dir/vf_inside_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp_in
+ abort_on_error midp $? clean_up_midp
+ clitkComposeVF -i $ref_vf_midp_out -j $vf_dir/vf_outside_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp_out
+ abort_on_error midp $? clean_up_midp
+
+ # combine in and out VF's
+ vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
+ clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
+ clitkZeroVF -i $vf_midp -o vf_zero.mhd
+ clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
+
+ midp=$midp_dir/midp_$phase_nb.mhd
+ clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
+ abort_on_error midp $? clean_up_midp
+
+ clitkImageConvert -i $midp -o $midp -t float
+ abort_on_error midp $? clean_up_midp
+ fi
+ done
+
+ rm vf_zero.*
+
+ # create 4D midp
+ create_mhd_4D_pattern.sh $midp_dir/midp_
+ create_mhd_4D_pattern.sh $midp_dir/vf_midp_
+ create_mhd_4D_pattern.sh $midp_dir/vf_inside_midp_
+ create_mhd_4D_pattern.sh $midp_dir/vf_outside_midp_
+
+ echo "Calculating midp_avg.mhd..."
+ clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+ abort_on_error midp $? clean_up_midp
+
+ echo "Calculating midp_med.mhd..."
+ clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
+ abort_on_error midp $? clean_up_midp
+
+ # clean-up
+ #rm $midp_dir/vf_*
+
+ echo
+ echo "-------- Mid-position done ! --------"
+ end=`date`
+ echo "start: $start"
+ echo "end: $end"
+ echo
+}
######################### main
@@ -257,8 +358,13 @@ if [ "$step" == "registration" -o "$step" == "all" ]; then
registration
fi
+midp_combined_vf=0
if [ "$step" == "midp" -o "$step" == "all" ]; then
- midp
+ if [ $midp_combined_vf = 0 ]; then
+ midp_in_out
+ else
+ midp
+ fi
fi
echo
http://git.creatis.insa-lyon.fr/pubgit/?p=clitk.git;a=commitdiff;h=dccc3844aeeffc19a6515e7e1969da7ce18c6698
commit dccc3844aeeffc19a6515e7e1969da7ce18c6698
Author: Romulo Pinho <romulo.pinho at lyon.unicancer.fr>
Date: Thu Dec 22 14:38:34 2011 +0100
use of coefficient images in mid-P creation
diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh
index 1f18830..3cd023c 100755
--- a/scripts/create_midP-2.0.sh
+++ b/scripts/create_midP-2.0.sh
@@ -41,6 +41,7 @@ registration()
banded=""
# params read from conf file
+ use_coeffs=1
params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
# register all phases to the reference
@@ -57,6 +58,10 @@ registration()
vf_in=$vf_dir/vf_inside_${ref_phase_nb}_$phase_nb.mhd
result_in=$output_dir/result_inside_${ref_phase_nb}_$phase_nb.mhd
log_in=$log_dir/log_inside_${ref_phase_nb}_$phase_nb.log
+ if [ $use_coeffs = 1 ]; then
+ init_coeff_in=$coeff_in # empty at first iteration
+ coeff_in=$vf_dir/coeff_inside_${ref_phase_nb}_$phase_nb.mhd
+ fi
# outside params
reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
@@ -66,11 +71,15 @@ registration()
vf_out=$vf_dir/vf_outside_$ref_phase_nb\_$phase_nb.mhd
result_out=$output_dir/result_outside_$ref_phase_nb\_$phase_nb.mhd
log_out=$log_dir/log_outside_${ref_phase_nb}_$phase_nb.log
+ if [ $use_coeffs = 1 ]; then
+ init_coeff_out=$coeff_out # empty at first iteration
+ coeff_out=$vf_dir/coeff_outside_${ref_phase_nb}_$phase_nb.mhd
+ fi
# registration
if [ "$method" == "blutdir" ]; then
- registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
- registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
+ registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in $coeff_in $init_coeff_in
+ registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out $init_coeff_out
elif [ "$method" == "elastix" ]; then
registration_elastix $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
diff --git a/scripts/registration.sh b/scripts/registration.sh
index 724e3ac..5431342 100755
--- a/scripts/registration.sh
+++ b/scripts/registration.sh
@@ -37,26 +37,37 @@ source `dirname $0`/midp_common.sh
################# BLUTDIR #####################
registration_blutdir()
{
- reference=$1
- target=$2
- mask_ref=$3
- mask_targ=$4
- vf=$5
- result=$6
- nb_iter=$7
- nb_samples=$8
- sampling_algo=$9
- hist_bins=${10}
- nb_levels=${11}
- spacing=${12}
- metric=${13}
- optimizer=${14}
- interpolator=${15}
- log=${16}
+ local reference=$1
+ local target=$2
+ local mask_ref=$3
+ local mask_targ=$4
+ local vf=$5
+ local result=$6
+ local nb_iter=$7
+ local nb_samples=$8
+ local sampling_algo=$9
+ local hist_bins=${10}
+ local nb_levels=${11}
+ local spacing=${12}
+ local metric=${13}
+ local optimizer=${14}
+ local interpolator=${15}
+ local log=${16}
+ local coeff=${17}
+ local init_coeff=${18}
echo "Computing BLUTDIR $reference -> $target ..."
blutdir_params="--levels $nb_levels --metric $metric --optimizer $optimizer --samples $nb_samples --spacing $spacing,$spacing,$spacing --bins $hist_bins --maxIt $nb_iter --interp $interpolator --verbose"
- cmd="clitkBLUTDIR -r $reference -t $target -m $mask_ref --targetMask $mask_targ --vf $vf -o $result $blutdir_params"
+
+ if [ -n "$coeff" ]; then
+ coeff="--coeff $coeff"
+ fi
+
+ if [ -n "$init_coeff" ]; then
+ init_coeff="--initCoeff $init_coeff"
+ fi
+
+ cmd="clitkBLUTDIR -r $reference -t $target -m $mask_ref --targetMask $mask_targ --vf $vf $coeff $init_coeff -o $result $blutdir_params"
$cmd > $log
abort_on_error registration_blutdir $? clean_up_registration
-----------------------------------------------------------------------
Summary of changes:
scripts/create_midP-2.0.sh | 121 ++++++++++++++++++++++++++++++++++++++++++-
scripts/registration.sh | 45 ++++++++++------
2 files changed, 146 insertions(+), 20 deletions(-)
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