diff --git a/DESCRIPTION b/DESCRIPTION index 4a2618d4..b0de5d18 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -44,7 +44,7 @@ Remotes: rstudio/keras SystemRequirements: Keras >= 2.0 (https://keras.io) Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.2 +RoxygenNote: 7.3.1 VignetteBuilder: knitr BugReports: https://github.com/ANTsX/ANTsRNet/issues URL: https://github.com/ANTsX/ANTsRNet diff --git a/NAMESPACE b/NAMESPACE index 27b36825..e160cb81 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -167,6 +167,7 @@ export(layer_spatial_transformer_3d) export(lesionSegmentation) export(linMatchIntensity) export(longitudinalCorticalThickness) +export(lungAirwaySegmentation) export(lungExtraction) export(lungPulmonaryArterySegmentation) export(masked_mse_error) diff --git a/R/getPretrainedNetwork.R b/R/getPretrainedNetwork.R index 7dd6afcf..98e63384 100644 --- a/R/getPretrainedNetwork.R +++ b/R/getPretrainedNetwork.R @@ -109,6 +109,7 @@ getPretrainedNetwork <- function( "protonLungMri", "protonLobes", "pulmonaryArteryWeights", + "pulmonaryAirwayWeights", "sixTissueOctantBrainSegmentation", "sixTissueOctantBrainSegmentationWithPriors1", "sixTissueOctantBrainSegmentationWithPriors2", @@ -227,6 +228,7 @@ getPretrainedNetwork <- function( mriModalityClassification = "https://figshare.com/ndownloader/files/41691681", protonLungMri = "https://ndownloader.figshare.com/files/13606799", protonLobes = "https://figshare.com/ndownloader/files/30678455", + pulmonaryAirwayWeights = "https://figshare.com/ndownloader/files/45187168", pulmonaryArteryWeights = "https://figshare.com/ndownloader/files/42918565", sixTissueOctantBrainSegmentation = "https://ndownloader.figshare.com/files/23776025", sixTissueOctantBrainSegmentationWithPriors1 = "https://ndownloader.figshare.com/files/28159869", diff --git a/man/getPretrainedNetwork.Rd b/man/getPretrainedNetwork.Rd index 8ae9c44a..bfaf00ff 100644 --- a/man/getPretrainedNetwork.Rd +++ b/man/getPretrainedNetwork.Rd @@ -31,18 +31,21 @@ getPretrainedNetwork( "hippMapp3rInitial", "hippMapp3rRefine", "hyperMapp3r", "hypothalamus", "inpainting_sagittal_rmnet_weights", "inpainting_coronal_rmnet_weights", - "inpainting_axial_rmnet_weights", "koniqMBCS", "koniqMS", "koniqMS2", "koniqMS3", + "inpainting_axial_rmnet_weights", "inpainting_axial_rmnet_flair_weights", + "inpainting_coronal_rmnet_flair_weights", "inpainting_sagittal_rmnet_flair_weights", + "koniqMBCS", "koniqMS", "koniqMS2", "koniqMS3", "lesion_whole_brain", "lungCtWithPriorsSegmentationWeights", "maskLobes", "mriSuperResolution", - "mriModalityClassification", "protonLungMri", "protonLobes", + "mriModalityClassification", "protonLungMri", "protonLobes", + "pulmonaryArteryWeights", "sixTissueOctantBrainSegmentation", "sixTissueOctantBrainSegmentationWithPriors1", - "sixTissueOctantBrainSegmentationWithPriors2", - "sysuMediaWmhFlairOnlyModel0", + "sixTissueOctantBrainSegmentationWithPriors2", "sysuMediaWmhFlairOnlyModel0", "sysuMediaWmhFlairOnlyModel1", "sysuMediaWmhFlairOnlyModel2", "sysuMediaWmhFlairT1Model0", "sysuMediaWmhFlairT1Model1", "sysuMediaWmhFlairT1Model2", "tidsQualityAssessment", "xrayLungOrientation", "xrayLungExtraction", "chexnetClassificationModel", - "chexnetClassificationANTsXNetModel", "wholeHeadInpaintingFLAIR", + "chexnetClassificationANTsXNetModel", "wholeHeadInpaintingFLAIR", + "wholeHeadInpaintingPatchBasedT1", "wholeHeadInpaintingPatchBasedFLAIR", "wholeTumorSegmentationT2Flair", "wholeLungMaskFromVentilation"), targetFileName, diff --git a/man/lungAirwaySegmentation.Rd b/man/lungAirwaySegmentation.Rd new file mode 100644 index 00000000..97db1814 --- /dev/null +++ b/man/lungAirwaySegmentation.Rd @@ -0,0 +1,53 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/lungSegmentation.R +\name{lungAirwaySegmentation} +\alias{lungAirwaySegmentation} +\title{Lung airway segmentation.} +\usage{ +lungAirwaySegmentation( + ct, + lungMask = NULL, + predictionBatchSize = 16, + patchStrideLength = 32, + antsxnetCacheDirectory = NULL, + verbose = FALSE +) +} +\arguments{ +\item{ct}{input 3-D ct image.} + +\item{lungMask}{input binary lung mask which defines the patch extraction +(label 1 = left lung, label 2 = right lung, label 3 = main airway). +If not supplied, one is estimated.} + +\item{predictionBatchSize}{Control memory usage for prediction. More consequential +for GPU-usage.} + +\item{patchStrideLength}{3-D vector or int. Dictates the stride length for +accumulating predicting patches.} + +\item{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 +inst/extdata/ subfolder of the ANTsRNet package.} + +\item{verbose}{print progress.} +} +\value{ +Probability image. +} +\description{ +Perform pulmonary artery segmentation. Training data taken from the +EXACT09 challenge (Lo, Pechin, et al. "Extraction of airways from CT +(EXACT'09)." https://pubmed.ncbi.nlm.nih.gov/22855226/) +} +\examples{ +\dontrun{ +library( ANTsRNet ) +library( keras ) + +} +} +\author{ +Tustison NJ +}