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Save DanaCase/9cfc23912fee48e437af03f97763d78e to your computer and use it in GitHub Desktop.
| import qupath.lib.scripting.QP | |
| import qupath.lib.geom.Point2 | |
| import qupath.lib.roi.PolygonROI | |
| import qupath.lib.objects.PathAnnotationObject | |
| import qupath.lib.images.servers.ImageServer | |
| //Aperio Image Scope displays images in a different orientation | |
| def rotated = true | |
| def server = QP.getCurrentImageData().getServer() | |
| def h = server.getHeight() | |
| def w = server.getWidth() | |
| // need to add annotations to hierarchy so qupath sees them | |
| def hierarchy = QP.getCurrentHierarchy() | |
| //Prompt user for exported aperio image scope annotation file | |
| def file = getQuPath().getDialogHelper().promptForFile('xml', null, 'aperio xml file', null) | |
| def text = file.getText() | |
| def list = new XmlSlurper().parseText(text) | |
| list.Annotation.each { | |
| it.Regions.Region.each { region -> | |
| def tmp_points_list = [] | |
| region.Vertices.Vertex.each{ vertex -> | |
| if (rotated) { | |
| X = vertex.@Y.toDouble() | |
| Y = h - vertex.@X.toDouble() | |
| } | |
| else { | |
| X = vertex.@X.toDouble() | |
| Y = vertex.@Y.toDouble() | |
| } | |
| tmp_points_list.add(new Point2(X, Y)) | |
| } | |
| def roi = new PolygonROI(tmp_points_list) | |
| def annotation = new PathAnnotationObject(roi) | |
| hierarchy.addPathObject(annotation, false) | |
| } | |
| } |
The latter error and the solution can be found on the image.sc forum.
I am not sure about the XmlSlurper though. It is likely due to reorganization of the functions used: https://stackoverflow.com/questions/55169114/unable-to-add-xmlslurper-to-eclipse-groovy-project
https://stackoverflow.com/questions/11245073/groovy-2-cant-find-jsonslurper-and-xmlslurper-anymore
Etc. I am not sure what the exact solution for QuPath will be.
Thanks for the answer. I have managed to make it work :
Here is the script that worked for me :
"import qupath.lib.scripting.QP
import qupath.lib.geom.Point2
import qupath.lib.roi.PolygonROI
import qupath.lib.objects.PathAnnotationObject
import qupath.lib.images.servers.ImageServer
//Aperio Image Scope displays images in a different orientation
def rotated = false
def server = QP.getCurrentImageData().getServer()
def h = server.getHeight()
def w = server.getWidth()
// need to add annotations to hierarchy so qupath sees them
def hierarchy = QP.getCurrentHierarchy()
//Prompt user for exported aperio image scope annotation file
def file = Dialogs.promptForFile('xml', null, 'aperio xml file', null)
def text = file.getText()
def list = new XmlSlurper().parseText(text)
list.Annotation.each {
it.Regions.Region.each { region ->
def tmp_points_list = []
region.Vertices.Vertex.each{ vertex ->
if (rotated) {
X = [email protected]()
Y = h - [email protected]()
}
else {
X = [email protected]()
Y = [email protected]()
}
tmp_points_list.add(new Point2(X, Y))
}
def roi = new PolygonROI(tmp_points_list)
def annotation = new PathAnnotationObject(roi)
hierarchy.addObject(annotation, false)
}
}"
I changed the following ::
replace getQuPath().getDialogHelper().promptForFile( with Dialogs.promptForFile(
replace hierarchy.addPathObject(annotation, false) with hierarchy.addObject(annotation, false)
Used version groovy-xml-3.0.17
Hope it helps
I can't launch this script. I've got the following errors :
With Qupath 0.4.3 : ERROR: It looks like you've tried to import a class 'XmlSlurper' that couldn't be found
With Qupath 0.2.3 : ERROR: MissingMethodException at line 20: No signature of method: qupath.lib.gui.QuPathGUI.getDialogHelper() is applicable for argument types: () values: []
Could you help
Thanks