patLanW | R Documentation |
Extracts color pattern from landmark transformed image using watershed segmentation. This function works interactively by allowing to pick a starting pixel within each pattern element from which the watershed will extract the pattern. This function works best for patterns with sharp boundaries.
patLanW(
sampleList,
landList,
IDlist = NULL,
adjustCoords = FALSE,
transformRef = "meanshape",
resampleFactor = NULL,
transformType = "tps",
maskOutline = NULL,
cartoonID = NULL,
correct = FALSE,
blur = TRUE,
sigma = 3,
bucketfill = TRUE,
cleanP = NULL,
splitC = NULL,
plotTransformed = FALSE,
plotCorrect = FALSE,
plotEdges = FALSE,
plotPriority = FALSE,
plotWS = FALSE,
plotBF = FALSE,
plotFinal = FALSE
)
sampleList |
List of RasterStack objects. |
landList |
Landmark list as returned by |
IDlist |
List of sample IDs should be specified when masking outline and transformRef is 'meanshape'. |
adjustCoords |
Adjust landmark coordinates in case they are reversed compared to pixel coordinates (default = FALSE). |
transformRef |
ID or landmark matrix of reference sample for shape to which color patterns will be transformed to. Can be 'meanshape' for transforming to mean shape of Procrustes analysis. |
resampleFactor |
Integer for downsampling image used by |
transformType |
Transformation type as used by |
maskOutline |
When outline is specified, everything outside of the outline will be masked for the color extraction (default = NULL). |
cartoonID |
ID of the sample for which the cartoon was drawn and will be used for masking (should be set when transformRef = 'meanShape'). |
correct |
Correct image illumination using a linear model (default = FALSE). |
blur |
Blur image for priority map extraction (default = TRUE). |
sigma |
Size of sigma for Gaussian blurring (default = 5). |
bucketfill |
Use a bucket fill on the background to fill holes (default = TRUE). |
cleanP |
Integer to remove spurious areas with width smaller than cleanP (default = NULL). |
splitC |
Integer to split selected patterns into connected components and remove ones with areas smaller than splitC (default = NULL). |
plotTransformed |
Plot transformed image (default = FALSE). |
plotCorrect |
Plot corrected image, corrected for illumination using a linear model (default = FALSE). |
plotEdges |
Plot image gradient (default = FALSE). |
plotPriority |
Plot priority map (default = FALSE). |
plotWS |
Plot watershed result (default = FALSE). |
plotBF |
Plot bucketfill (default = FALSE). |
plotFinal |
Plot extracted patterns (default = FALSE). |
List of raster objects.
## Not run:
IDlist <- c('BC0077','BC0071','BC0050','BC0049','BC0004')
prepath <- system.file("extdata", package = 'patternize')
extension <- '_landmarks_LFW.txt'
landmarkList <- makeList(IDlist, 'landmark', prepath, extension)
extension <- '.jpg'
imageList <- makeList(IDlist, 'image', prepath, extension)
outline_BC0077 <- read.table(paste(system.file("extdata", package = 'patternize'),
'/BC0077_outline.txt', sep=''), header = FALSE)
rasterList_W <- patLanW(imageList, landmarkList, IDlist, transformRef = 'meanshape',
adjustCoords = TRUE, plotTransformed = FALSE, correct = TRUE, plotCorrect = FALSE, blur = FALSE,
sigma = 2, bucketfill = FALSE, cleanP = 0, splitC = 10, plotPriority = TRUE, plotWS = TRUE,
plotBF = TRUE, plotFinal = TRUE, maskOutline = outline_BC0077, cartoonID = 'BC0077')
## End(Not run)
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