ENH: Allow user to control averaging method in initial stages

After the initial average which sets the template volume size, users can now control mean / norm mean / median. Added a summarizeimageset function to antsMultivariateTemplateConstruction.sh, which makes it easier and more consistent to update the template. Added some additional checks to both scripts to ensure that the template actually gets updated properly, using all the images it ought to have.
gandreadis · Aug 23, 2021 · 14853e4 · 14853e4
1 parent f3390d4
commit 14853e4
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diff --git a/Scripts/antsMultivariateTemplateConstruction.sh b/Scripts/antsMultivariateTemplateConstruction.sh
@@ -255,6 +255,75 @@ function reportMappingParameters {
 REPORTMAPPINGPARAMETERS
 }
 
+function summarizeimageset() {
+
+  local dim=$1
+  shift
+  local output=$1
+  shift
+  local summarizemethod=$1
+  shift
+  local sharpenmethod=$1
+  shift
+  local images=( "${@}" )
+
+  if [[ ${#images[@]} -ne ${IMAGESPERMODALITY} ]]
+    then
+      echo "ERROR summarizeimageset - imagelist length is ${#images[@]}, expected ${IMAGESPERMODALITY}"
+      exit 1
+    fi
+
+  rm -f "$output"
+
+  case $summarizemethod in
+    0) #mean
+      ${ANTSPATH}/AverageImages $dim $output 0 ${images[@]}
+      ;;
+    1) #mean of normalized images
+      ${ANTSPATH}/AverageImages $dim $output 2 ${images[@]}
+      ;;
+    2) #median
+      local image
+      for image in "${images[@]}";
+        do
+          echo $image >> ${output}_list.txt
+        done
+      ${ANTSPATH}/ImageSetStatistics $dim ${output}_list.txt ${output} 0
+      rm ${output}_list.txt
+      ;;
+  esac
+
+  if [[ ! -f "$output" ]];
+    then
+      echo "summarizeimageset: ERROR - output file $output could not be created"
+      exit 1
+    fi
+
+  case $sharpenmethod in
+    0)
+      echo "Sharpening method none"
+      ;;
+    1)
+      echo "Laplacian sharpening"
+      ${ANTSPATH}/ImageMath $dim $output Sharpen $output
+      ;;
+    2)
+      echo "Unsharp mask sharpening"
+      ${ANTSPATH}/ImageMath $dim $output UnsharpMask $output 0.5 1 0 0
+      ;;
+  esac
+
+  local sharpenExit=$?
+
+  if [[ $? -ne 0 ]]
+    then
+      echo "summarizeimageset: ERROR - template sharpening failed with status $?"
+      exit 1
+    fi
+
+}
+
+
 function shapeupdatetotemplate() {
 
    echo "shapeupdatetotemplate()"
@@ -286,46 +355,13 @@ function shapeupdatetotemplate() {
     echo "--------------------------------------------------------------------------------------"
 
     imagelist=(`ls ${outputname}template${whichtemplate}*WarpedToTemplate.nii.gz`)
-    if [[ ${#imagelist[@]} -ne ${IMAGESPERMODALITY} ]] ; then
-      echo "ERROR shapeupdatedtotemplate - imagelist length is ${#imagelist[@]}, expected ${IMAGESPERMODALITY}"
-      exit 1
-    fi
-
-    case $summarizemethod in
-    0) #mean
-      ${ANTSPATH}/AverageImages $dim ${template} 0 ${templatename}${whichtemplate}*WarpedToTemplate.nii.gz
-      ;;
-    1) #mean of normalized images
-      ${ANTSPATH}/AverageImages $dim ${template} 2 ${templatename}${whichtemplate}*WarpedToTemplate.nii.gz
-      ;;
-    2) #median
-      local image
-      for image in ${templatename}${whichtemplate}*WarpedToTemplate.nii.gz;
-        do
-          echo $image >> ${templatename}${whichtemplate}_list.txt
-        done
-      ${ANTSPATH}/ImageSetStatistics $dim ${templatename}${whichtemplate}_list.txt ${template} 0
-      rm ${templatename}${whichtemplate}_list.txt
-      ;;
-  esac
-
-    echo "--------------------------------------------------------------------------------------"
-    echo " shapeupdatetotemplate---sharpening of the new template"
-    echo "--------------------------------------------------------------------------------------"
+    if [[ ${#imagelist[@]} -ne ${IMAGESPERMODALITY} ]]
+      then
+        echo "ERROR shapeupdatedtotemplate - imagelist length is ${#imagelist[@]}, expected ${IMAGESPERMODALITY}"
+        exit 1
+      fi
 
-    case $sharpenmethod in
-    0)
-      echo "Sharpening method none"
-      ;;
-    1)
-      echo "Laplacian sharpening"
-      ${ANTSPATH}/ImageMath $dim $template Sharpen $template
-      ;;
-    2)
-      echo "Unsharp mask sharpening"
-      ${ANTSPATH}/ImageMath $dim $template UnsharpMask $template 0.5 1 0 0
-      ;;
-  esac
+    summarizeimageset ${dim} ${template} ${summarizemethod} ${sharpenmethod} ${imagelist[@]}
 
     if [[ $whichtemplate -eq 0 ]] ;
       then
@@ -897,8 +933,9 @@ for (( i = 0; i < $NUMBEROFMODALITIES; i++ ))
         echo " Creating template ${TEMPLATES[$i]} from a population average image from the inputs."
         echo "   ${CURRENTIMAGESET[@]}"
         echo "--------------------------------------------------------------------------------------"
-        # Normalize but don't sharpen at this stage
-        ${ANTSPATH}/AverageImages $DIM ${TEMPLATES[$i]} 2 ${CURRENTIMAGESET[@]}
+        # Normalized mean, no sharpening
+        # This forces a call to AverageImages, which resizes images to match the largest input
+        summarizeimageset $DIM ${TEMPLATES[$i]} 1 0 ${CURRENTIMAGESET[@]}
         # Quickly align COM of input images to average, and then recompute average
         IMAGECOMSET=()
         for (( j = 0; j < ${#CURRENTIMAGESET[@]}; j+=1 ))
@@ -912,7 +949,8 @@ for (( i = 0; i < $NUMBEROFMODALITIES; i++ ))
             rm -f $COMTRANSFORM
             IMAGECOMSET[${#IMAGECOMSET[@]}]=$COM
           done
-          ${ANTSPATH}/AverageImages $DIM ${TEMPLATES[$i]} 2 ${IMAGECOMSET[@]}
+          # Now safe to let user control stat method
+          summarizeimageset $DIM ${TEMPLATES[$i]} ${STATSMETHOD} 0 ${IMAGECOMSET[@]}
           # Clean up
           rm -f ${IMAGECOMSET[@]}
     fi
@@ -1119,7 +1157,7 @@ if [[ "$RIGID" -eq 1 ]];
         echo  "${ANTSPATH}/AverageImages $DIM ${TEMPLATES[$j]} 2 ${IMAGERIGIDSET[@]}"
 
       # Don't sharpen after rigid alignment
-      ${ANTSPATH}/AverageImages $DIM ${TEMPLATES[$j]} 2 ${IMAGERIGIDSET[@]}
+      summarizeimageset $DIM ${TEMPLATES[$j]} ${STATSMETHOD} 0 ${IMAGERIGIDSET[@]}
       intermediateTemplateBase=`basename ${TEMPLATES[$j]}`
       cp ${TEMPLATES[$j]} ${intermediateTemplateDir}/initialRigid_${intermediateTemplateBase}
 

diff --git a/Scripts/antsMultivariateTemplateConstruction2.sh b/Scripts/antsMultivariateTemplateConstruction2.sh
@@ -322,14 +322,22 @@ function summarizeimageset() {
   shift
   local sharpenmethod=$1
   shift
-  local images=( "${@}" "" )
+  local images=( "${@}" )
+
+  if [[ ${#images[@]} -ne ${IMAGESPERMODALITY} ]]
+    then
+      echo "ERROR summarizeimageset - imagelist length is ${#images[@]}, expected ${IMAGESPERMODALITY}"
+      exit 1
+    fi
+
+  rm -f "$output"
 
   case $summarizemethod in
     0) #mean
-      ${ANTSPATH}/AverageImages $dim $output 0 ${images[*]}
+      ${ANTSPATH}/AverageImages $dim $output 0 ${images[@]}
       ;;
     1) #mean of normalized images
-      ${ANTSPATH}/AverageImages $dim $output 2 ${images[*]}
+      ${ANTSPATH}/AverageImages $dim $output 2 ${images[@]}
       ;;
     2) #median
       local image
@@ -342,6 +350,12 @@ function summarizeimageset() {
       ;;
   esac
 
+  if [[ ! -f "$output" ]];
+    then
+      echo "summarizeimageset: ERROR - output file $output could not be created"
+      exit 1
+    fi
+
   case $sharpenmethod in
     0)
       echo "Sharpening method none"
@@ -355,7 +369,16 @@ function summarizeimageset() {
       ${ANTSPATH}/ImageMath $dim $output UnsharpMask $output 0.5 1 0 0
       ;;
   esac
-  }
+
+  local sharpenExit=$?
+
+  if [[ $? -ne 0 ]]
+    then
+      echo "summarizeimageset: ERROR - template sharpening failed with status $?"
+      exit 1
+    fi
+
+}
 
 function shapeupdatetotemplate() {
 
@@ -391,10 +414,11 @@ function shapeupdatetotemplate() {
     echo "--------------------------------------------------------------------------------------"
 
     imagelist=(`ls ${outputname}template${whichtemplate}*WarpedToTemplate.nii.gz`)
-    if [[ ${#imagelist[@]} -ne ${IMAGESPERMODALITY} ]] ; then
-      echo "ERROR shapeupdatedtotemplate - imagelist length is ${#imagelist[@]}, expected ${IMAGESPERMODALITY}"
-      exit 1
-    fi
+    if [[ ${#imagelist[@]} -ne ${IMAGESPERMODALITY} ]]
+      then
+        echo "ERROR shapeupdatedtotemplate - imagelist length is ${#imagelist[@]}, expected ${IMAGESPERMODALITY}"
+        exit 1
+      fi
 
     summarizeimageset $dim $template $statsmethod $sharpenmethod ${imagelist[@]}
 
@@ -1062,6 +1086,7 @@ for (( i = 0; i < $NUMBEROFMODALITIES; i++ ))
         echo "   ${CURRENTIMAGESET[@]}"
         echo "--------------------------------------------------------------------------------------"
         # Normalized mean, no sharpening
+        # This forces a call to AverageImages, which resizes images to match the largest input
         summarizeimageset $DIM ${TEMPLATES[$i]} 1 0 ${CURRENTIMAGESET[@]}
         # Quickly align COM of input images to average, and then recompute average
         IMAGECOMSET=()
@@ -1076,8 +1101,8 @@ for (( i = 0; i < $NUMBEROFMODALITIES; i++ ))
             rm -f $COMTRANSFORM
             IMAGECOMSET[${#IMAGECOMSET[@]}]=$COM
           done
-        # Could let user control statmethod here, but set to normalized mean for consistency with antsMultivariateTemplate.sh
-        summarizeimageset $DIM ${TEMPLATES[$i]} 1 0 ${IMAGECOMSET[@]}
+        # Now safe to let user control stat method
+        summarizeimageset $DIM ${TEMPLATES[$i]} $STATSMETHOD 0 ${IMAGECOMSET[@]}
         # Clean up
         rm -f ${IMAGECOMSET[@]}
       fi
@@ -1291,9 +1316,8 @@ if [[ "$RIGID" -eq 1 ]];
         echo
         echo  "Building rigid template from ${IMAGERIGIDSET[@]}"
 
-        # Could let user control statmethod here, but set to normalized mean for consistency with antsMultivariateTemplate.sh
         # No sharpening at rigid stage
-        summarizeimageset $DIM ${TEMPLATES[$j]} 1 0 ${IMAGERIGIDSET[@]}
+        summarizeimageset $DIM ${TEMPLATES[$j]} $STATSMETHOD 0 ${IMAGERIGIDSET[@]}
         intermediateTemplateBase=`basename ${TEMPLATES[$j]}`
         cp ${TEMPLATES[$j]} ${intermediateTemplateDir}/initialRigid_${intermediateTemplateBase}