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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,134 @@ | ||
| #' Check x-ray lung orientation. | ||
| #' | ||
| #' Check the correctness of image orientation, i.e., flipped left-right, up-down, | ||
| #' or both. If True, attempts to correct before returning corrected image. Otherwise | ||
| #' it returns NULL. | ||
| #' | ||
| #' @param image input 3-D lung image. | ||
| #' @param antsxnetCacheDirectory destination directory for storing the downloaded | ||
| #' template and model weights. Since these can be resused, if | ||
| #' \code{is.null(antsxnetCacheDirectory)}, these data will be downloaded to the | ||
| #' subdirectory ~/.keras/ANTsXNet/. | ||
| #' @param verbose print progress. | ||
| #' @return segmentation and probability images | ||
| #' @author Tustison NJ | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' library( ANTsRNet ) | ||
| #' } | ||
| #' @import keras | ||
| #' @export | ||
| checkXrayLungOrientation <- function( image, | ||
| antsxnetCacheDirectory = NULL, | ||
| verbose = FALSE ) | ||
| { | ||
| if( image@dimension != 2 ) | ||
| { | ||
| stop( "ImageDimension must be equal to 2.") | ||
| } | ||
|
|
||
| resampledImageSize <- c( 224, 224 ) | ||
| if( any( dim( image ) != resampledImageSize ) ) | ||
| { | ||
| if( verbose ) | ||
| { | ||
| cat( "Resampling image to ", resampledImageSize, "\n" ) | ||
| } | ||
| resampledImage <- resampleImage( image, resampledImageSize, useVoxels = TRUE ) | ||
| } | ||
| else | ||
| { | ||
| resampledImage <- antsImageClone( image ) | ||
| } | ||
|
|
||
| model <- createResNetModel2D( c( resampledImageSize, 1 ), | ||
| numberOfClassificationLabels = 3, | ||
| mode = "classification", | ||
| layers = c( 1, 2, 3, 4 ), | ||
| residualBlockSchedule = c( 2, 2, 2, 2 ), | ||
| lowestResolution = 64, | ||
| cardinality = 1, | ||
| squeezeAndExcite = FALSE ) | ||
|
|
||
| weightsFileName <- getPretrainedNetwork( "xrayLungOrientation", | ||
| antsxnetCacheDirectory = antsxnetCacheDirectory ) | ||
| model$load_weights( weightsFileName ) | ||
|
|
||
| imageMin <- min( resampledImage ) | ||
| imageMax <- max( resampledImage ) | ||
| normalizedImage <- antsImageClone( resampledImage ) | ||
| normalizedImage <- ( normalizedImage - imageMin ) / ( imageMax - imageMin ) | ||
|
|
||
| batchX <- array( data = as.array( normalizedImage ), dim = c( 1, resampledImageSize, 1 ) ) | ||
| batchY <- model %>% predict( batchX, verbose = verbose ) | ||
|
|
||
| # batchY is a 3-element array: | ||
| # batchY[0] = Pr(image is correctly oriented) | ||
| # batchY[1] = Pr(image is flipped up/down) | ||
| # batchY[2] = Pr(image is flipped left/right) | ||
|
|
||
| if( batchY[1, 1] > 0.5 ) | ||
| { | ||
| return( NULL ) | ||
| } else { | ||
| if( verbose ) | ||
| { | ||
| message( "Possible incorrect orientation. Attempting to correct." ) | ||
| } | ||
| normalizedImageArray <- as.array( normalizedImage ) | ||
| imageUpDown <- as.antsImage( normalizedImageArray[,dim( normalizedImageArray )[2]:1], | ||
| origin = antsGetOrigin( resampledImage ), | ||
| spacing = antsGetSpacing( resampledImage ), | ||
| direction = antsGetDirection( resampledImage ) ) | ||
| imageLeftRight <- as.antsImage( normalizedImageArray[dim( normalizedImageArray )[1]:1,], | ||
| origin = antsGetOrigin( resampledImage ), | ||
| spacing = antsGetSpacing( resampledImage ), | ||
| direction = antsGetDirection( resampledImage ) ) | ||
| imageBoth <- as.antsImage( ( normalizedImageArray[,dim( normalizedImageArray )[2]:1] )[dim( normalizedImageArray )[1]:1,], | ||
| origin = antsGetOrigin( resampledImage ), | ||
| spacing = antsGetSpacing( resampledImage ), | ||
| direction = antsGetDirection( resampledImage ) ) | ||
|
|
||
| batchX <- array( data = 0, dim = c( 3, resampledImageSize, 1 ) ) | ||
| batchX[1,,,1] <- as.array( imageUpDown ) | ||
| batchX[2,,,1] <- as.array( imageLeftRight ) | ||
| batchX[3,,,1] <- as.array( imageBoth ) | ||
|
|
||
| batchY <- model %>% predict( batchX, verbose = verbose ) | ||
|
|
||
| imageArray <- as.array( image ) | ||
| orientedImage <- NULL | ||
| if( batchY[1, 1] > batchY[2, 1] && batchY[1, 1] > batchY[3, 1] ) | ||
| { | ||
| if( verbose ) | ||
| { | ||
| message( "Image is flipped up-down." ) | ||
| } | ||
| orientedImage <- as.antsImage( imageArray[,dim( imageArray )[2]:1], | ||
| origin = antsGetOrigin( image ), | ||
| spacing = antsGetSpacing( image ), | ||
| direction = antsGetDirection( image ) ) | ||
| } else if( batchY[2, 1] > batchY[1, 1] && batchY[2, 1] > batchY[3, 1] ) { | ||
| if( verbose ) | ||
| { | ||
| message( "Image is flipped right-left." ) | ||
| } | ||
| orientedImage <- as.antsImage( imageArray[dim( imageArray )[1]:1,], | ||
| origin = antsGetOrigin( image ), | ||
| spacing = antsGetSpacing( image ), | ||
| direction = antsGetDirection( image ) ) | ||
| } else { | ||
| if( verbose ) | ||
| { | ||
| message( "Image is flipped up-down and right-left." ) | ||
| } | ||
| orientedImage <- as.antsImage( ( imageArray[,dim( imageArray )[2]:1] )[dim( imageArray )[1]:1,], | ||
| origin = antsGetOrigin( image ), | ||
| spacing = antsGetSpacing( image ), | ||
| direction = antsGetDirection( image ) ) | ||
| } | ||
|
|
||
| return( orientedImage ) | ||
| } | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| pandoc: '0' | ||
| pkgdown: 2.0.6 | ||
| pkgdown: 1.6.1 | ||
| pkgdown_sha: ~ | ||
| articles: {} | ||
| last_built: 2023-09-09T00:57Z | ||
| last_built: 2023-09-25T22:03Z | ||
|
|
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