Merge pull request #410 from ANTsX/LabelReg

ntustison · web-flow · commit fc554893da86 · 2024-11-24T19:09:43.000-08:00
ENH:  Add label image registration.
diff --git a/NAMESPACE b/NAMESPACE
@@ -233,6 +233,7 @@ export(knnSmoothingMatrix)
 export(labelClusters)
 export(labelGeometryMeasures)
 export(labelImageCentroids)
+export(labelImageRegistration)
 export(labelOverlapMeasures)
 export(labelStats)
 export(labels2matrix)
diff --git a/R/labelImageRegistration.R b/R/labelImageRegistration.R
@@ -0,0 +1,390 @@
+#' Perform label image registration.
+#'
+#' Perform pairwise registration using fixed and moving sets of label 
+#' images (and, optionally, sets of corresponding intensity images).
+#'
+#' @param fixedLabelImages A single (or set of) fixed label image(s).
+#' @param movingLabelImages A single (or set of) moving label image(s).
+#' @param fixedIntensityImages Optional---a single (or set of) fixed 
+#' intensity image(s).
+#' @param movingIntensityImages Optional---a single (or set of) moving 
+#' intensity image(s).
+#' @param fixedMask Defines region for similarity metric calculation 
+#' in the space of the fixed image.
+#' @param movingMask Defines region for similarity metric calculation 
+#' in the space of the moving image.
+#' @param typeOfLinearTransform Use label images with the centers of 
+#' mass to a calculate linear transform of type \code{'rigid'}, 
+#' \code{'similarity'}, \code{'affine'}.
+#' @param typeOfTransform Only works with deformable-only transforms, 
+#' specifically the family of \code{antsRegistrationSyN*[so]} or 
+#' \code{antsRegistrationSyN*[bo]} transforms.  See 'type_of_transform' 
+#' in \code{antsRegistration}.
+#' @param labelImageWeighting Float or vector of floats giving the relative 
+#' weighting for the label images.
+#' @param outputPrefix String definining the output prefix for the filenames
+#' of the output transform files.
+#' @param randomSeed Definition for deformable registration.
+#' @param verbose Print progress to the screen.
+#' @return outputs a list containing:
+#' \itemize{
+#'   \item{fwdtransforms: }{Transforms to move from moving to fixed image.}
+#'   \item{invtransforms: }{Transforms to move from fixed to moving image.}
+#' }
+#' Output of 1 indicates failure.
+#' @author Tustison NJ
+#' @examples
+#' \dontrun{
+#' r16 <- antsImageRead( getANTsRData( "r16" ) )
+#' r16Seg1 <- thresholdImage( r16, "Kmeans", 3 ) - 1
+#' r16Seg2 <- thresholdImage( r16, "Kmeans", 5 ) - 1
+#' r64 <- antsImageRead( getANTsRData( "r64" ) )
+#' r64Seg1 <- thresholdImage( r64, "Kmeans", 3 ) - 1
+#' r64Seg2 <- thresholdImage( r64, "Kmeans", 5 ) - 1
+#' reg <- labelImageRegistration( list( r16Seg1, r16Seg2 ),
+#'                                      list( r64Seg1, r64Seg2 ),  
+#'                                      fixedIntensityImages = r16,
+#'                                      movingIntensityImages = r64,
+#'                                      typeOfLinearTransform = 'affine',
+#'                                      typeOfTransform = 'antsRegistrationSyNQuick[bo]',
+#'                                      labelImageWeighting = c( 1.0, 2.0 ),
+#'                                      verbose = TRUE )
+#' }
+#'
+#' @export labelImageRegistration
+labelImageRegistration <- function( fixedLabelImages, movingLabelImages,
+    fixedIntensityImages = NULL, movingIntensityImages = NULL,
+    fixedMask = NULL, movingMask = NULL,
+    typeOfLinearTransform = 'affine', 
+    typeOfTransform = 'antsRegistrationSyNQuick[so]',
+    labelImageWeighting = 1.0,
+    outputPrefix = '',
+    randomSeed = NULL, 
+    verbose = FALSE )
+{     
+  # Preform validation check on the input
+
+  if( ANTsR::is.antsImage( fixedLabelImages ) )
+    {
+    fixedLabelImages <- list( antsImageClone( fixedLabelImages ) )
+    }
+  if( ANTsR::is.antsImage( movingLabelImages ) )
+    {
+    movingLabelImages <- list( antsImageClone( movingLabelImages ) )
+    }
+
+  if( length( fixedLabelImages ) != length( movingLabelImages ) ) 
+    {
+    stop( "The number of fixed and moving label images do not match." )
+    }
+  
+  if( ! is.null( fixedIntensityImages ) || ! is.null( movingIntensityImages ) )
+    {
+    if( ANTsR::is.antsImage( fixedIntensityImages ) )
+      {
+      fixedIntensityImages <- list( antsImageClone( fixedIntensityImages ) )
+      }
+    if( ANTsR::is.antsImage( movingIntensityImages ) )
+      {
+      movingIntensityImages <- list( antsImageClone( movingIntensityImages ) )
+      }
+    if( length( fixedIntensityImages ) != length( movingIntensityImages ) ) 
+      {
+      stop( "The number of fixed and moving intensity images do not match." )
+      }
+    }
+    
+  labelImageWeights <- labelImageWeighting
+  if( is.numeric( labelImageWeighting ) && ! is.vector( labelImageWeighting ) )
+    {
+    labelImageWeights <- rep( labelImageWeighting, length( fixedLabelImages ) ) 
+    } else {
+    if( length( fixedLabelImages ) != length( labelImageWeights ) )
+      {
+      stop( paste( "The length of labelImageWeights must",
+                   "match the number of label image pairs." ) )
+      }
+    }
+
+  imageDimension <- fixedLabelImages[[1]]@dimension
+
+  if( outputPrefix == '' || is.null( outputPrefix ) || length( outputPrefix ) == 0 )
+    {
+    outputPrefix <- tempfile()
+    }
+
+  allowableLinearTransforms <- c( 'rigid', 'similarity', 'affine' )
+  if( ! typeOfLinearTransform %in% allowableLinearTransforms )
+    {
+    stop( "Unrecognized linear transform." ) 
+    }
+
+  doDeformable <- FALSE
+  if( ! is.null( typeOfTransform ) || length( typeOfTransform ) > 0 )
+    {
+    doDeformable <- TRUE 
+    }
+
+  commonLabelIds <- list()
+  totalNumberOfLabels <- 0
+  for( i in seq.int( length( fixedLabelImages ) ) )
+    {
+    fixedLabelGeoms <- labelGeometryMeasures( fixedLabelImages[[i]] )
+    fixedLabelIds <-fixedLabelGeoms$Label
+    movingLabelGeoms <- labelGeometryMeasures( movingLabelImages[[i]] )
+    movingLabelIds <- movingLabelGeoms$Label
+    commonLabelIds[[i]] <- intersect( fixedLabelIds, movingLabelIds )
+    totalNumberOfLabels = totalNumberOfLabels + length( commonLabelIds[[i]] )
+    if( verbose )
+      {
+      message( paste0( "Common label ids for image pair ", i, ": ", commonLabelIds[i] ) ) 
+      }
+    if( length( commonLabelIds[[i]]) == 0 )
+      {
+      stop( paste0( "No common labels for image pair ", i ) )
+      }
+    }
+  
+  if( verbose )
+    {
+    message( "Total number of labels: ", totalNumberOfLabels )
+    }
+
+  ##############################
+  #
+  #    Linear transform
+  #
+  ##############################
+
+  linearXfrm <- NULL
+  if( ! is.null( typeOfLinearTransform ) )
+    {
+    if( verbose )
+      {
+      message( "\n\nComputing linear transform.\n" )
+      }
+
+    if( totalNumberOfLabels < 3 )
+      {
+      stop( "  Number of labels must be >= 3." ) 
+      }  
+
+    fixedCentersOfMass <- array( data = 0, c( totalNumberOfLabels, imageDimension ) )  
+    movingCentersOfMass <- array( data = 0, c( totalNumberOfLabels, imageDimension ) )  
+
+    deformableMultivariateExtras <- list()
+
+    count <- 1
+    for( i in seq.int( length( commonLabelIds ) ) )
+      {
+      for( j in seq.int( length( commonLabelIds[[i]] ) ) )
+        {
+        label <- commonLabelIds[[i]][j]
+        if( verbose )
+          {
+          message( paste0( "  Finding centers of mass for image pair ", i, ", label ", label ) )
+          }
+        fixedSingleLabelImage <- thresholdImage( fixedLabelImages[[i]], label, label, 1, 0 )  
+        fixedCentersOfMass[count,] <- getCenterOfMass( fixedSingleLabelImage )
+        movingSingleLabelImage <- thresholdImage( movingLabelImages[[i]], label, label, 1, 0 )  
+        movingCentersOfMass[count,] <- getCenterOfMass( movingSingleLabelImage )
+        count <- count + 1
+        if( doDeformable ) 
+          {
+          deformableMultivariateExtras[[i]] <- list( "MSQ", fixedSingleLabelImage,
+                                                     movingSingleLabelImage, 
+                                                     labelImageWeights[i], 0)
+          }
+        } 
+      }
+
+    linearXfrm <- fitTransformToPairedPoints( movingCentersOfMass, 
+                                              fixedCentersOfMass, 
+                                              transformType = typeOfLinearTransform,
+                                              verbose = verbose )
+
+    linearXfrmFile <- paste0( outputPrefix, "0GenericAffine.mat" )
+    writeAntsrTransform( linearXfrm, linearXfrmFile )
+    }
+
+  ##############################
+  #
+  #    Deformable transform
+  #
+  ##############################
+
+  if( doDeformable )
+    {
+    if( verbose )
+      {
+      message( "\n\nComputing deformable transform using images.\n" )
+      }
+
+    doQuick <- FALSE
+    doRepro <- FALSE 
+
+    if( grepl( "Quick", typeOfTransform ) )
+      {
+      doQuick <- TRUE
+      } else {
+      doRepro <- TRUE
+      randomSeed <- 1
+      }
+
+    intensityMetricParameter <- NULL
+    splineDistance <- 26
+    if( grepl( "\\[", typeOfTransform ) && grepl("\\]", typeOfTransform ) ) 
+      {
+      subtypeOfTransform <- strsplit( strsplit( typeOfTransform, "\\[")[[1]][2], "\\]" )[[1]][1]
+      if( ! ( grepl( "bo", subtypeOfTransform ) || grepl( "so", subtypeOfTransform ) ) )
+        {
+        stop( "Only 'so' or 'bo' transforms are available." ) 
+        }
+      if( grepl( ",", subtypeOfTransform ) ) 
+        {
+        subtypeOfTransformArgs <- strsplit( subtypeOfTransform, "," )[[1]]
+        subtypeOfTransform <- subtypeOfTransformArgs[1]
+        intensityMetricParameter <- subtypeOfTransformArgs[2]
+        if( length( subtypeOfTransformArgs ) > 2 ) 
+          {
+          splineDistance <- subtypeOfTransformArgs[3]
+          }
+        }
+      }
+
+    synTransform <- "SyN[0.1,3,0]"
+    if( subtypeOfTransform == "bo" ) 
+      {
+      synTransform <- paste0("BSplineSyN[0.1,", splineDistance, ",0,3]")
+      }
+    synStage <- list( "--transform", synTransform )
+
+    if( doQuick ) 
+      {
+      synConvergence <- "[100x70x50x0,1e-6,10]"
+      } else {
+        synConvergence <- "[100x70x50x20,1e-6,10]"
+      }
+    synShrinkFactors <- "8x4x2x1"
+    synSmoothingSigmas <- "3x2x1x0vox"
+
+    synStage <- lappend( synStage, list(
+      "--convergence", synConvergence,
+      "--shrink-factors", synShrinkFactors,
+      "--smoothing-sigmas", synSmoothingSigmas
+      ) )
+
+    intensityMetric <- NULL
+    if( ! is.null( fixedIntensityImages ) && ! is.null( movingIntensityImages ) )
+      {
+      if( doQuick )
+        {
+        intensityMetric <- "MI" 
+        if( is.null( intensityMetricParameter ) )
+          {
+          intensityMetricParameter <- 32 
+          }
+        }
+      if( ! doQuick || doRepro )
+        {
+        intensityMetric <- "CC" 
+        if( is.null( intensityMetricParameter ) )
+          {
+          intensityMetricParameter <- 2
+          }
+        }
+      for( i in seq.int( length( fixedIntensityImages ) ) )  
+        {
+        synStage <- lappend( synStage, list(
+            "--metric", paste0( intensityMetric, "[",
+              antsrGetPointerName( fixedIntensityImages[[i]] ), ",",
+              antsrGetPointerName( movingIntensityImages[[i]] ), ",",
+              "1.0,", as.character( intensityMetricParameter ), "]" ) ) )  
+        }
+      }
+    for( kk in seq.int( length( deformableMultivariateExtras ) ) )
+      {
+      synStage <- lappend( synStage, list(
+          "--metric", paste0( "MSQ[",
+            antsrGetPointerName( deformableMultivariateExtras[[kk]][[2]] ), ",",
+            antsrGetPointerName( deformableMultivariateExtras[[kk]][[3]] ), ",",
+            as.character( deformableMultivariateExtras[[kk]][[4]] ), ",0.0]" ) ) )  
+      } 
+
+    args <- NULL
+    if( is.null( linearXfrm ) )
+      {
+      args <- list(
+        "-d", as.character( imageDimension ),
+        "-o", outputPrefix )
+      } else {
+      args <- list(
+        "-d", as.character( imageDimension ),
+        "-r", linearXfrmFile,
+        "-o", outputPrefix )
+      }
+    args <- lappend( args, synStage ) 
+
+    fixedMaskString <- "NA"
+    if( ! is.null( fixedMask ) )
+      {
+      fixedMaskBinary <- antsImageClone( thresholdImage( fixedMask, 0, 0, 0, 1), "unsigned char" ) 
+      fixedMaskString <- antsrGetPointerName( fixedMaskBinary )
+      }
+
+    movingMaskString <- "NA"
+    if( ! is.null( movingMask ) )
+      {
+      movingMaskBinary <- antsImageClone( thresholdImage( movingMask, 0, 0, 0, 1), "unsigned char" ) 
+      movingMaskString <- antsrGetPointerName( movingMaskBinary )
+      }
+
+    maskOption <- paste0( "[", fixedMaskString, ",", movingMaskString, "]" )
+    args <- lappend( args, list( "-x", maskOption ) )
+
+    args <- lappend( args, list( "--float", "1" ) )
+
+    if( ! is.null( randomSeed ) )
+      {
+      args <- lappend( "--random-seed", randomSeed )
+      }
+
+    if( verbose )  
+      {
+      args <- lappend( args, list( "-v", "1" ) )
+      cat( "antsRegistration", paste( unlist( args ) ), "\n" )
+      }
+    args <- .int_antsProcessArguments( c( args ) )
+    ANTsRCore::AntsRegistration( args )
+    }
+
+  allXfrms <- Sys.glob( paste0( outputPrefix, "*", "[0-9]*" ) )
+
+  findInverseWarps <- grep( "[0-9]InverseWarp.nii.gz", allXfrms )
+  findForwardWarps <- grep( "[0-9]Warp.nii.gz", allXfrms )
+
+  if( length( findInverseWarps ) > 0 ) 
+    {
+    fwdtransforms <- c( allXfrms[findForwardWarps[1]], linearXfrmFile ) 
+    invtransforms <- c( linearXfrmFile, allXfrms[findInverseWarps[1]] ) 
+    } else {
+    fwdtransforms <- c( linearXfrmFile ) 
+    invtransforms <- c( linearXfrmFile ) 
+    }
+
+  if( verbose )
+    {
+    message( "\n\nResulting transforms" )   
+    if( length( findInverseWarps ) > 0 ) 
+      {
+      message( paste0( "  fwdtransforms: [", fwdtransforms[1], ", ", fwdtransforms[2], "]" ) )
+      message( paste0( "  invtransforms: [", invtransforms[1], ", ", invtransforms[2], "]" ) )
+      } else {
+      message( paste0( "  fwdtransforms: [", fwdtransforms[1], "]" ) )
+      message( paste0( "  invtransforms: [", invtransforms[1], "]" ) )
+      }
+    }
+
+  return( list( fwdtransforms = fwdtransforms,
+                invtransforms = invtransforms ) )
+}
diff --git a/man/labelImageRegistration.Rd b/man/labelImageRegistration.Rd
