Note however that not everything can be converted to JSON.įor example, you can’t do this with an object hierarchy or an ImageData. getMetadata ()) print 'Metadata IS the same' else print 'Metadata IS NOT the same'įiguring out a JSON way to represent ImageServers has taken up rather a lot of my time recently… but so far this seems to be working. class if ( server = server2 ) print 'Servers ARE the same' else print 'Servers ARE NOT the same' if ( server.
fromJson ( json, ImageServer ) print server print server. toJson ( getCurrentServer ()) def server2 = gson. getInstance ( prettyPrint ) def server = getCurrentServer () def json = gson. Import .ImageServer import .GsonTools boolean prettyPrint = true def gson = GsonTools. calibrateImagePlus ( imp, request, server ) imp. matToImagePlus ( mat, "My image" ) IJTools. close () // Convert Mat to an ImagePlus, setting pixel calibration info & then show it def imp = OpenCVTools.
clone () GaussianBlur ( mat, mat2, new Size ( 15, 15 ), 2.0 ) GaussianBlur ( mat, mat, new Size ( 15, 15 ), 1.0 ) subtract ( mat, mat2, mat ) mat2. readBufferedImage ( request ) // Convert to an OpenCV Mat, then apply a difference of Gaussians filter def mat = OpenCVTools. getPath (), downsample, roi ) def img = server. * import ij.* // Read BufferedImage region def server = getCurrentServer () def roi = getSelectedROI () double downsample = 4.0 def request = RegionRequest. Import .* import import import _core.Size import static org. Often we don’t need the PathImage wrapper, but here we keep it so that we can pass it to nvertToIJRoi(roi, pathImage) later. This is basically a wrapper for an image of some kind (here, an ImageJ ImagePlus) along with some calibration information. This introduces another class: PathImage. show () // Convert QuPath ROI to ImageJ Roi & add to open image def roiIJ = IJTools. convertToImagePlus ( server, request ) def imp = pathImage. getPath (), downsample, roi ) def pathImage = IJTools. getImageJInstance () // Read image & show in ImageJ def server = getCurrentServer () def roi = getSelectedROI () double downsample = 4.0 def request = RegionRequest. Import .* import import import ij.* // Request an ImageJ instance - this will open the GUI if necessary // This isn't essential, but makes it it possible to interact with any image that is shown IJExtension.
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