MNT: replace dc calls with syntax that will work on all platforms ("dc -" is

unsupported on new macOS)

MNT: replace dc calls with syntax that will work on all platforms ("dc -" is
4820d213 · Paul McCarthy · 11c9cd5b · 4820d213 · 4820d213 · 4820d213
Commit 4820d213 authored 2 years ago by Paul McCarthy
--- a/siena
+++ b/siena
@@ -80,13 +80,13 @@ while [ _$1 != _ ] ; do
    elif [ $1 = -t ] ; then
 	dostd=1
 	stdt=`echo $2 | sed 's/-/_/g'`
-	stdt=`echo "10 k $stdt $pixdim3 / $origin3 + p" | dc -`
+	stdt=`echo "10 k $stdt $pixdim3 / $origin3 + p" | dc`
 	stdroi="$stdroi -roi 0 1000000 0 1000000 0 $stdt 0 1"
 	shift 2
    elif [ $1 = -b ] ; then
 	dostd=1
 	stdb=`echo $2 | sed 's/-/_/g'`
-	stdb=`echo "10 k $stdb $pixdim3 / $origin3 + p" | dc -`
+	stdb=`echo "10 k $stdb $pixdim3 / $origin3 + p" | dc`
 	stdroi="$stdroi -roi 0 1000000 0 1000000 $stdb 1000000 0 1"
 	shift 2
    elif [ $1 = -V ] ; then
@@ -112,7 +112,7 @@ fi
 sdo="${sdo}${is_t2}"

 mkdir -p $outdir
-if [ $do_viena = yes ] ; then 
+if [ $do_viena = yes ] ; then
  mkdir -p $vienadir
 fi
 ${FSLDIR}/bin/imcp $Ao ${outdir}/A
@@ -151,13 +151,13 @@ echo "<hr><p><b>FLIRT A-to-B registration results</b><p><IMG BORDER=0 SRC=\"${A}

 echo ""                                                                        >> report.siena
 echo "----------  produce valid masks  --------------------------------------" >> report.siena
-XDIM=`${FSLDIR}/bin/fslval $A dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
-YDIM=`${FSLDIR}/bin/fslval $A dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
-ZDIM=`${FSLDIR}/bin/fslval $A dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
+XDIM=`${FSLDIR}/bin/fslval $A dim1` ; XDIM=`echo "$XDIM 2 - p" | dc`
+YDIM=`${FSLDIR}/bin/fslval $A dim2` ; YDIM=`echo "$YDIM 2 - p" | dc`
+ZDIM=`${FSLDIR}/bin/fslval $A dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc`
 ${FSLDIR}/bin/fslmaths ${A}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${A}_valid_mask
-XDIM=`${FSLDIR}/bin/fslval $B dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
-YDIM=`${FSLDIR}/bin/fslval $B dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
-ZDIM=`${FSLDIR}/bin/fslval $B dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
+XDIM=`${FSLDIR}/bin/fslval $B dim1` ; XDIM=`echo "$XDIM 2 - p" | dc`
+YDIM=`${FSLDIR}/bin/fslval $B dim2` ; YDIM=`echo "$YDIM 2 - p" | dc`
+ZDIM=`${FSLDIR}/bin/fslval $B dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc`
 ${FSLDIR}/bin/fslmaths ${B}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${B}_valid_mask
 ${FSLDIR}/bin/flirt -in ${B}_valid_mask -ref $A -out ${B}_valid_mask_to_${A} -applyxfm -init ${B}_to_${A}.mat -paddingsize 0
 ${FSLDIR}/bin/flirt -in ${A}_valid_mask -ref $B -out ${A}_valid_mask_to_${B} -applyxfm -init ${A}_to_${B}.mat -paddingsize 0
@@ -213,7 +213,7 @@ echo ""                                                                        >
 echo "----------  change analysis  ------------------------------------------" >> report.siena
 corr1=`${FSLDIR}/bin/siena_cal $A $B 1.002 $sdo $sdopts`
 corr2=`${FSLDIR}/bin/siena_cal $B $A 1.002 $sdo $sdopts`
-corr=`echo "10 k $corr1 $corr2 + 2.0 / p" | dc -`
+corr=`echo "10 k $corr1 $corr2 + 2.0 / p" | dc`
 echo "corr1=$corr1 corr2=$corr2 corr=$corr" >> report.siena

 echo "" >> report.siena
@@ -232,7 +232,7 @@ pbvc_forward=`grep PBVC report.siena | tail -n 1 | awk '{print $2}' | sed 's/-/_
 echo "<hr><p><b>FAST tissue segmentation</b><br>These images show the tissue segmentation used to find the brain/non-brain boundary. The exact segmentation of grey matter vs. white matter is not important.<p>${Ao}<br><IMG BORDER=0 SRC=\"${A}_halfwayto_${B}_brain_seg.png\"><p>${Bo}<br><IMG BORDER=0 SRC=\"${B}_halfwayto_${A}_brain_seg.png\">" >> report.html

 echo "" >> report.siena
-pbvc_average=`echo "10 k $pbvc_forward $pbvc_backward - 2.0 / p" | dc -`
+pbvc_average=`echo "10 k $pbvc_forward $pbvc_backward - 2.0 / p" | dc`
 echo "finalPBVC $pbvc_average %" >> report.siena

 ${FSLDIR}/bin/fslmaths ${A}_to_${B}_flow -mul -1 ${A}_to_${B}_flowneg
@@ -246,7 +246,7 @@ echo "<hr><p><b>Final brain edge movement image</b><p>atrophy <IMG SRC=\".ramp2.

 if [ $do_viena = yes ] ; then

-    # Export Ao and Bo (containing the input file names) as they 
+    # Export Ao and Bo (containing the input file names) as they
    # are used in viena_quant during HTML report generation
    export Ao
    export Bo
@@ -348,4 +348,3 @@ volume change between the two timepoints.
 <BR>&nbsp;&nbsp;&nbsp;IEEE Trans. on Medical Imaging, 20(1):45-57, 2001.

 EOF
-
--- a/siena_cal
+++ b/siena_cal
@@ -24,7 +24,7 @@ input=`${FSLDIR}/bin/remove_ext $1`
 inputB=`${FSLDIR}/bin/remove_ext $2`

 m=$3
-M=`echo "5 k 1.0 $m / p" | dc -`
+M=`echo "5 k 1.0 $m / p" | dc`
 shift 3

 o1=`${FSLDIR}/bin/fslval ${input} dim1`
@@ -35,18 +35,18 @@ v1=`${FSLDIR}/bin/fslval ${input} pixdim1 | sed "s/-//g"`
 v2=`${FSLDIR}/bin/fslval ${input} pixdim2 | sed "s/-//g"`
 v3=`${FSLDIR}/bin/fslval ${input} pixdim3 | sed "s/-//g"`

-t1=`echo "5 k $m 1.0 - $o1 * $v1 * _0.5 * p" | dc -`
-t2=`echo "5 k $m 1.0 - $o2 * $v2 * _0.5 * p" | dc -`
-t3=`echo "5 k $m 1.0 - $o3 * $v3 * _0.5 * p" | dc -`
+t1=`echo "5 k $m 1.0 - $o1 * $v1 * _0.5 * p" | dc`
+t2=`echo "5 k $m 1.0 - $o2 * $v2 * _0.5 * p" | dc`
+t3=`echo "5 k $m 1.0 - $o3 * $v3 * _0.5 * p" | dc`

 echo "$m  0.0 0.0 $t1" >  ${input}_halfwayto_sc${input}.mat
 echo "0.0 $m  0.0 $t2" >> ${input}_halfwayto_sc${input}.mat
 echo "0.0 0.0 $m  $t3" >> ${input}_halfwayto_sc${input}.mat
 echo "0.0 0.0 0.0 1.0" >> ${input}_halfwayto_sc${input}.mat

-t1=`echo "5 k $M 1.0 - $o1 * $v1 * _0.5 * p" | dc -`
-t2=`echo "5 k $M 1.0 - $o2 * $v2 * _0.5 * p" | dc -`
-t3=`echo "5 k $M 1.0 - $o3 * $v3 * _0.5 * p" | dc -`
+t1=`echo "5 k $M 1.0 - $o1 * $v1 * _0.5 * p" | dc`
+t2=`echo "5 k $M 1.0 - $o2 * $v2 * _0.5 * p" | dc`
+t3=`echo "5 k $M 1.0 - $o3 * $v3 * _0.5 * p" | dc`

 echo "$M  0.0 0.0 $t1" >  sc${input}_halfwayto_${input}.mat
 echo "0.0 $M  0.0 $t2" >> sc${input}_halfwayto_${input}.mat
@@ -59,9 +59,9 @@ $FSLDIR/bin/imcp ${input}_valid_mask_with_$inputB ${input}_valid_mask_with_sc$in

 ${FSLDIR}/bin/siena_diff ${input} sc${input} $@ > ${input}_to_sc${input}.siena

-vm=`echo "10 k $m 6 ^ 1.0 - 100.0 * p" | dc -`
+vm=`echo "10 k $m 6 ^ 1.0 - 100.0 * p" | dc`
 cal=`grep PBVC ${input}_to_sc${input}.siena | awk '{print $2}' | sed "s/-//g"`
-corr=`echo "10 k $vm $cal / p" | dc -`
+corr=`echo "10 k $vm $cal / p" | dc`

 #echo "$m $vm $cal $corr"
 echo $corr
@@ -78,4 +78,3 @@ $FSLDIR/bin/imrm sc${input}.* \

 /bin/rm -f ${input}_halfwayto_sc${input}.mat sc${input}_halfwayto_${input}.mat \
           ${input}_to_sc${input}.siena ${input}_halfwayto_sc${input}_brain.vol
-
--- a/sienax
+++ b/sienax
@@ -70,12 +70,12 @@ while [ _$1 != _ ] ; do
        shift
    elif [ $1 = -t ] ; then
 	stdt=`echo $2 | sed 's/-/_/g'`
-	stdt=`echo "10 k $stdt $pixdim3 / $origin3 + p" | dc -`
+	stdt=`echo "10 k $stdt $pixdim3 / $origin3 + p" | dc`
 	stdroi="$stdroi -roi 0 1000000 0 1000000 0 $stdt 0 1"
 	shift 2
    elif [ $1 = -b ] ; then
 	stdb=`echo $2 | sed 's/-/_/g'`
-	stdb=`echo "10 k $stdb $pixdim3 / $origin3 + p" | dc -`
+	stdb=`echo "10 k $stdb $pixdim3 / $origin3 + p" | dc`
 	stdroi="$stdroi -roi 0 1000000 0 1000000 $stdb 1000000 0 1"
 	shift 2
    elif [ $1 = -lm ] ; then
@@ -129,7 +129,7 @@ ${FSLDIR}/bin/avscale ${I}2std.mat ${FSLDIR}/data/standard/MNI152_T1_2mm > ${I}2
 xscale=`grep Scales ${I}2std.avscale | awk '{print $4}'`
 yscale=`grep Scales ${I}2std.avscale | awk '{print $5}'`
 zscale=`grep Scales ${I}2std.avscale | awk '{print $6}'`
-vscale=`echo "10 k $xscale $yscale * $zscale * p"|dc -`
+vscale=`echo "10 k $xscale $yscale * $zscale * p"|dc`
 echo "VSCALING $vscale" >> report.sienax
 ${FSLDIR}/bin/flirt -in $I -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -o ${I}2std -applyxfm -init ${I}2std.mat
 ${FSLDIR}/bin/slicer ${I}2std ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -a ${I}2std.png
@@ -172,8 +172,8 @@ if [ $nseg = 2 ] ; then
    S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_1 -m -v`
    xa=`echo $S | awk '{print $1}'`
    xb=`echo $S | awk '{print $3}'`
-    ubrain=`echo "2 k $xa $xb * 1 / p" | dc -`
-    nbrain=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
+    ubrain=`echo "2 k $xa $xb * 1 / p" | dc`
+    nbrain=`echo "2 k $xa $xb * $vscale * 1 / p" | dc`
 else
    if [ _$lm != _ ] ; then
 	${FSLDIR}/bin/fslmaths $lm -bin -mul -1 -add 1 -mul ${I}_stdmaskbrain ${I}_stdmaskbrain -odt float
@@ -195,33 +195,33 @@ else
 	S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_1_segperiph -m -v`
 	xa=`echo $S | awk '{print $1}'`
 	xb=`echo $S | awk '{print $3}'`
-	uxg=`echo "2 k $xa $xb * 1 / p" | dc -`
-	xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
+	uxg=`echo "2 k $xa $xb * 1 / p" | dc`
+	xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc`
 	echo "pgrey              $xg $uxg (peripheral grey)" >> report.sienax

 	${FSLDIR}/bin/fslmaths ${I}_stdmaskbrain_pve_0 -mas ${I}_stdmask_segvent ${I}_stdmaskbrain_pve_0_segvent -odt float
 	S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_0_segvent -m -v`
 	xa=`echo $S | awk '{print $1}'`
 	xb=`echo $S | awk '{print $3}'`
-	uxg=`echo "2 k $xa $xb * 1 / p" | dc -`
-	xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
+	uxg=`echo "2 k $xa $xb * 1 / p" | dc`
+	xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc`
 	echo "vcsf               $xg $uxg (ventricular CSF)" >> report.sienax
    fi
    S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_1 -m -v`
    xa=`echo $S | awk '{print $1}'`
    xb=`echo $S | awk '{print $3}'`
-    ugrey=`echo "2 k $xa $xb * 1 / p" | dc -`
-    ngrey=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
+    ugrey=`echo "2 k $xa $xb * 1 / p" | dc`
+    ngrey=`echo "2 k $xa $xb * $vscale * 1 / p" | dc`
    echo "GREY               $ngrey $ugrey" >> report.sienax
    S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_2 -m -v`
    xa=`echo $S | awk '{print $1}'`
    xb=`echo $S | awk '{print $3}'`
-    uwhite=`echo "2 k $xa $xb * 1 / p" | dc -`
-    nwhite=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
+    uwhite=`echo "2 k $xa $xb * 1 / p" | dc`
+    nwhite=`echo "2 k $xa $xb * $vscale * 1 / p" | dc`
    echo "WHITE              $nwhite $uwhite" >> report.sienax

-    ubrain=`echo "2 k $uwhite $ugrey + 1 / p" | dc -`
-    nbrain=`echo "2 k $nwhite $ngrey + 1 / p" | dc -`
+    ubrain=`echo "2 k $uwhite $ugrey + 1 / p" | dc`
+    nbrain=`echo "2 k $nwhite $ngrey + 1 / p" | dc`
 fi

 echo "BRAIN              $nbrain $ubrain" >> report.sienax
@@ -308,4 +308,3 @@ ventricular CSF).
 <BR>&nbsp;&nbsp;&nbsp;IEEE Trans. on Medical Imaging, 20(1):45-57, 2001.

 EOF
-
--- a/viena_quant
+++ b/viena_quant
@@ -126,17 +126,17 @@ edgepointsbase=`${FSLDIR}/bin/fslstats ${scbaseedge}_ventricles -V | cut -d' ' -
 infobaseflow=`${FSLDIR}/bin/fslstats ${scbaseflow}_ventricles -V -M`
 nonzeroflowbase=`echo ${infobaseflow} | cut -d' ' -f1`
 tempmeanflowbase=`echo ${infobaseflow} | cut -d' ' -f3`
-meanflowbase=`echo "10 k ${tempmeanflowbase} ${nonzeroflowbase} * ${edgepointsbase} / p" | sed 's/-/_/g' | dc -`
+meanflowbase=`echo "10 k ${tempmeanflowbase} ${nonzeroflowbase} * ${edgepointsbase} / p" | sed 's/-/_/g' | dc`

 # Determine only one of three pixdims because we have isotropic pixels.
 pixdimbase=`${FSLDIR}/bin/fslval ${scbasehalf} pixdim1`

 # Calculate PVVC
-temppvvcbase=`echo "10 k 30 ${pixdimbase} * ${meanflowbase} * p" | sed 's/-/_/g' | dc -`
+temppvvcbase=`echo "10 k 30 ${pixdimbase} * ${meanflowbase} * p" | sed 's/-/_/g' | dc`

 # We assume standard FSL settings have been used, i.e. 0.2% change for calibration, change above if not true.
-vm=`echo "10 k ${m} 6 ^ 1.0 - 100.0 * p" | dc -`
-calibbase=`echo "10 k ${vm} ${temppvvcbase} / p" | sed 's/-/_/g' | dc -`
+vm=`echo "10 k ${m} 6 ^ 1.0 - 100.0 * p" | dc`
+calibbase=`echo "10 k ${vm} ${temppvvcbase} / p" | sed 's/-/_/g' | dc`

 echo "edgepointsbase ${edgepointsbase}"     >> "$LOG"
 echo "infobaseflow ${infobaseflow}"         >> "$LOG"
@@ -159,17 +159,17 @@ edgepointsfollow=`${FSLDIR}/bin/fslstats ${scfollowedge}_ventricles -V|cut -f 1
 infofollowflow=`${FSLDIR}/bin/fslstats ${scfollowflow}_ventricles -V -M`
 nonzeroflowfollow=`echo ${infofollowflow} | cut -d' ' -f1`
 tempmeanflowfollow=`echo ${infofollowflow} | cut -d' ' -f3`
-meanflowfollow=`echo "10 k ${tempmeanflowfollow} ${nonzeroflowfollow} * ${edgepointsfollow} / p" | sed 's/-/_/g' | dc -`
+meanflowfollow=`echo "10 k ${tempmeanflowfollow} ${nonzeroflowfollow} * ${edgepointsfollow} / p" | sed 's/-/_/g' | dc`

 # Determine only one of three pixdims because we have isotropic pixels.
 pixdimfollow=`${FSLDIR}/bin/fslval ${scfollowhalf} pixdim1`

 # Calculate PVVC
-temppvvcfollow=`echo "10 k 30 ${pixdimfollow} * ${meanflowfollow} * p" | sed 's/-/_/g' | dc -`
+temppvvcfollow=`echo "10 k 30 ${pixdimfollow} * ${meanflowfollow} * p" | sed 's/-/_/g' | dc`

 # We assume standard FSL settings have been used, i.e. 0.2% change for calibration, change above if not true.
-vm=`echo "10 k ${m} 6 ^ 1.0 - 100.0 * p" | dc -`
-calibfollow=`echo "10 k ${vm} ${temppvvcfollow} / p" | sed 's/-/_/g' | dc -`
+vm=`echo "10 k ${m} 6 ^ 1.0 - 100.0 * p" | dc`
+calibfollow=`echo "10 k ${vm} ${temppvvcfollow} / p" | sed 's/-/_/g' | dc`

 echo "edgepointsfollow ${edgepointsfollow}"     >> "$LOG"
 echo "infofollowflow ${infofollowflow}"         >> "$LOG"
@@ -207,25 +207,25 @@ edgepointsbase=`${FSLDIR}/bin/fslstats ${base}_to_${follow}_edgepoints_ventricle
 infobaseflow=`${FSLDIR}/bin/fslstats ${base}_to_${follow}_flow_ventricles -V -M`
 nonzeroflowbase=`echo ${infobaseflow}|cut -f 1 -d " "`
 tempmeanflowbase=`echo ${infobaseflow}|cut -f 3 -d " "`
-meanflowbase=`echo "10 k ${tempmeanflowbase} ${nonzeroflowbase} * ${edgepointsbase} / p" | sed 's/-/_/g' | dc -`
+meanflowbase=`echo "10 k ${tempmeanflowbase} ${nonzeroflowbase} * ${edgepointsbase} / p" | sed 's/-/_/g' | dc`
 pixdimbase=`${FSLDIR}/bin/fslval ${base}_halfwayto_${follow} pixdim1`

 edgepointsfollow=`${FSLDIR}/bin/fslstats ${follow}_to_${base}_edgepoints_ventricles -V|cut -f 1 -d " "`
 infofollowflow=`${FSLDIR}/bin/fslstats ${follow}_to_${base}_flow_ventricles -V -M`
 nonzeroflowfollow=`echo ${infofollowflow} | cut -f 1 -d " "`
 tempmeanflowfollow=`echo ${infofollowflow} | cut -f 3 -d " "`
-meanflowfollow=`echo "10 k ${tempmeanflowfollow} ${nonzeroflowfollow} * ${edgepointsfollow} / p" | sed 's/-/_/g' | dc -`
+meanflowfollow=`echo "10 k ${tempmeanflowfollow} ${nonzeroflowfollow} * ${edgepointsfollow} / p" | sed 's/-/_/g' | dc`
 pixdimfollow=`${FSLDIR}/bin/fslval ${follow}_halfwayto_${base} pixdim1`

 # Calculate PVVC base -> follow
-pvvcbasetofollow=`echo "10 k 30 ${calibbase} * ${pixdimbase} * ${meanflowbase} * _1.0 * p" | sed 's/-/_/g' | dc -`
+pvvcbasetofollow=`echo "10 k 30 ${calibbase} * ${pixdimbase} * ${meanflowbase} * _1.0 * p" | sed 's/-/_/g' | dc`

 # Calculate PVVC follow -> base
-pvvcfollowtobase=`echo "10 k 30 ${calibfollow} * ${pixdimfollow} * ${meanflowfollow} * _1.0 * p" | sed 's/-/_/g' | dc -`
-denom=`echo "10 k ${pvvcfollowtobase} 100 / 1.0 + p" | sed 's/-/_/g' | dc -`
-tmpbackwards=`echo "10 k ${pvvcfollowtobase} ${denom} / _1.0 * p" |sed 's/-/_/g' | dc -`
+pvvcfollowtobase=`echo "10 k 30 ${calibfollow} * ${pixdimfollow} * ${meanflowfollow} * _1.0 * p" | sed 's/-/_/g' | dc`
+denom=`echo "10 k ${pvvcfollowtobase} 100 / 1.0 + p" | sed 's/-/_/g' | dc`
+tmpbackwards=`echo "10 k ${pvvcfollowtobase} ${denom} / _1.0 * p" |sed 's/-/_/g' | dc`

-meanpvvc=`echo "10 k ${pvvcbasetofollow} ${tmpbackwards} + 2 / p" | sed 's/-/_/g' | dc -`
+meanpvvc=`echo "10 k ${pvvcbasetofollow} ${tmpbackwards} + 2 / p" | sed 's/-/_/g' | dc`

 echo ""                 >> "$LOG"
 echo ""                 >> "$LOG"