From: Romulo Pinho Date: Wed, 22 Feb 2012 09:49:06 +0000 (+0100) Subject: replaced deprecated clitk tools in midP creation X-Git-Tag: v1.3.0~88 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=a3b837ce11b76111761bd519d48bce7881b630c3;p=clitk.git replaced deprecated clitk tools in midP creation --- diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh index 3b943d3..7af8b09 100755 --- a/scripts/create_midP-2.0.sh +++ b/scripts/create_midP-2.0.sh @@ -89,19 +89,22 @@ registration() # combine in and out results out_result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd - clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result + # clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result + combine_image $result_in $result_out $out_result $motion_mask abort_on_error registration $? clean_up_registration # combine in and out vf vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd - clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result + #clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result + combine_image $vf_in $vf_out $vf_result $motion_mask abort_on_error registration $? clean_up_registration clitkZeroVF -i $vf_in -o vf_zero.mhd abort_on_error registration $? clean_up_registration patient_mask=$mask_dir/patient_mask_$phase_nb.mhd - clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result + #clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result + combine_image $vf_result vf_zero.mhd $vf_result $patient_mask abort_on_error registration $? clean_up_registration rm vf_zero.* @@ -123,7 +126,8 @@ registration() reference_in=$mask_dir/${banded}inside_${ref_phase_nb}.mhd reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd out_result=$output_dir/result_${ref_phase_nb}_${ref_phase_nb}.mhd - clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result + #clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result + combine_image $reference_in $reference_out $out_result $motion_mask abort_on_error registration $? clean_up_registration # create 4D vf @@ -164,7 +168,8 @@ midp() vf_midp=$midp_dir/vf_midp_$phase_nb.mhd midp=$midp_dir/midp_$phase_nb.mhd # average the vf's from reference phase to phase - clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp + #clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp + average_temporal_dimension $vf_dir/vf_${ref_phase_nb}_4D.mhd $vf_midp abort_on_error midp $? clean_up_midp # invert the vf (why?) @@ -207,7 +212,8 @@ midp() create_mhd_4D_pattern.sh $midp_dir/vf_midp_ echo "Calculating midp_avg.mhd..." - clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd + #clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd + average_temporal_dimension $midp_dir/midp_4D.mhd $midp_dir/midp_avg.mhd abort_on_error midp $? clean_up_midp echo "Calculating midp_med.mhd..." @@ -245,10 +251,12 @@ midp_in_out() coeff_midp_out=$midp_dir/coeff_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 - clitkAverageTemporalDimension -i $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_in + #clitkAverageTemporalDimension -i $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_in + average_temporal_dimension $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd $coeff_midp_in abort_on_error midp $? clean_up_midp # clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out - clitkAverageTemporalDimension -i $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_out + #clitkAverageTemporalDimension -i $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_out + average_temporal_dimension $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd $coeff_midp_out abort_on_error midp $? clean_up_midp # invert the vf @@ -263,9 +271,11 @@ midp_in_out() ref_vf_midp_in=$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 + #clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd + combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/mm_$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 + #clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd + combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd # create the midp by warping the reference phase with the reference vf midp=$midp_dir/midp_$phase_nb.mhd @@ -293,9 +303,11 @@ midp_in_out() # 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 + #clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd + combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/mm_$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 + #clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd + combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd midp=$midp_dir/midp_$phase_nb.mhd clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1 @@ -315,7 +327,8 @@ midp_in_out() 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 + #clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd + average_temporal_dimension $midp_dir/midp_4D.mhd $midp_dir/midp_avg.mhd abort_on_error midp $? clean_up_midp echo "Calculating midp_med.mhd..." diff --git a/scripts/midp_common.sh b/scripts/midp_common.sh index aa500ae..16535a1 100755 --- a/scripts/midp_common.sh +++ b/scripts/midp_common.sh @@ -173,3 +173,37 @@ extract_4d_phases_ref() fi done } + +# +# replacement for clitkCombineImage +combine_image() +{ +# eg: -i $result_in -j $result_out -o $out_result -m $motion_mask + + clitkSetBackground -i $1 -o temp1.mhd -m $4 + clitkSetBackground -i $2 -o temp2.mhd -m $4 --fg + + clitkImageArithm -i temp1.mhd -j temp2.mhd -o $3 + rm temp?.* +} + +# +# replacement for clitkAverageTemporalDimension +average_temporal_dimension() +{ + # eg: -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd + + local tot=tot.mhd + + local dir=`dirname $1` + local first=`grep raw $1 | sed 's/raw/mhd/g' | head -n 1` + clitkImageArithm -i $dir/$first -o $tot -t 1 -s 0 + + local nbphases=`grep raw $1 | sed 's/raw/mhd/g' | wc -l` + for i in $(grep raw $1 | sed 's/raw/mhd/g'); do + clitkImageArithm -i $dir/$i -j $tot -o $tot + done + + clitkImageArithm -i $tot -o $2 -t 11 -s $nbphases + rm tot.* +}